diff --git a/Projects/Incomplete/AVRISP/AVRISP.c b/Projects/Incomplete/AVRISP/AVRISP.c
index 403db314e20e4f122a40ef0d460c25c5c074f55b..f14b6545a1feb22bd77438f15f5d6b3d896508ea 100644
--- a/Projects/Incomplete/AVRISP/AVRISP.c
+++ b/Projects/Incomplete/AVRISP/AVRISP.c
@@ -34,11 +34,9 @@
  *  the project and is responsible for the initial application hardware configuration.
  */
 
-// TODO: Fix PROGRAM FLASH and PROGRAM EEPROM command processing
 // TODO: Add in software SPI for lower programming speeds below 125KHz
 // TODO: Add in VTARGET detection
 // TODO: Add reversed target connector checks
-// TODO: Add Doxygen comments to functions
 
 #include "AVRISP.h"
 
diff --git a/Projects/Incomplete/AVRISP/Lib/V2Protocol.c b/Projects/Incomplete/AVRISP/Lib/V2Protocol.c
index 08a54e2f1386739ca9ac2e97ad6adb7b9d73f075..248c50d245c26b3f19b7e95c15bab308d1753c97 100644
--- a/Projects/Incomplete/AVRISP/Lib/V2Protocol.c
+++ b/Projects/Incomplete/AVRISP/Lib/V2Protocol.c
@@ -36,6 +36,10 @@
 #define  INCLUDE_FROM_V2PROTOCOL_C
 #include "V2Protocol.h"
 
+/** Master V2 Protocol packet handler, for receieved V2 Protocol packets from a connected host.
+ *  This routine decodes the issued command and passes off the handling of the command to the
+ *  appropriate function.
+ */
 void V2Protocol_ProcessCommand(void)
 {
 	uint8_t V2Command = Endpoint_Read_Byte();
@@ -94,6 +98,11 @@ void V2Protocol_ProcessCommand(void)
 	Endpoint_SetEndpointDirection(ENDPOINT_DIR_OUT);
 }
 
+/** Handler for unknown V2 protocol commands. This discards all sent data and returns a
+ *  STATUS_CMD_UNKNOWN status back to the host.
+ *
+ *  \param V2Command  Issued V2 Protocol command byte from the host
+ */
 static void V2Protocol_Command_Unknown(uint8_t V2Command)
 {
 	/* Discard all incomming data */
@@ -110,7 +119,8 @@ static void V2Protocol_Command_Unknown(uint8_t V2Command)
 	Endpoint_Write_Byte(STATUS_CMD_UNKNOWN);
 	Endpoint_ClearIN();
 }
-
+
+/** Handler for the CMD_SIGN_ON command, returning the programmer ID string to the host. */
 static void V2Protocol_Command_SignOn(void)
 {
 	Endpoint_ClearOUT();
@@ -123,6 +133,11 @@ static void V2Protocol_Command_SignOn(void)
 	Endpoint_ClearIN();
 }
 
+/** Handler for the CMD_SET_PARAMETER and CMD_GET_PARAMETER commands from the host, setting or
+ *  getting a device parameter's value from the parameter table.
+ *
+ *  \param V2Command  Issued V2 Protocol command byte from the host
+ */
 static void V2Protocol_Command_GetSetParam(uint8_t V2Command)
 {
 	uint8_t ParamID = Endpoint_Read_Byte();
@@ -156,6 +171,10 @@ static void V2Protocol_Command_GetSetParam(uint8_t V2Command)
 	Endpoint_ClearIN();
 }
 
+/** Handler for the CMD_LOAD_ADDRESS command, loading the given device address into a
+ *  global storage variable for later use, and issuing LOAD EXTENDED ADDRESS commands
+ *  to the attached device as required.
+ */
 static void V2Protocol_Command_LoadAddress(void)
 {
 	Endpoint_Read_Stream_BE(&CurrentAddress, sizeof(CurrentAddress));
@@ -171,6 +190,9 @@ static void V2Protocol_Command_LoadAddress(void)
 	Endpoint_ClearIN();
 }
 
+/** Handler for the CMD_RESET_PROTECTION command, currently implemented as a dummy ACK function
+ *  as no ISP short-circuit protection is currently implemented.
+ */
 static void V2Protocol_Command_ResetProtection(void)
 {
 	Endpoint_ClearOUT();
@@ -181,6 +203,9 @@ static void V2Protocol_Command_ResetProtection(void)
 	Endpoint_ClearIN();	
 }
 
+/** Handler for the CMD_ENTER_PROGMODE_ISP command, which attempts to enter programming mode on
+ *  the attached device, returning success or failure back to the host.
+ */
 static void V2Protocol_Command_EnterISPMode(void)
 {
 	struct
@@ -237,6 +262,7 @@ static void V2Protocol_Command_EnterISPMode(void)
 	Endpoint_ClearIN();
 }
 
+/** Handler for the CMD_LEAVE_ISP command, which releases the target from programming mode. */
 static void V2Protocol_Command_LeaveISPMode(void)
 {
 	struct
@@ -260,6 +286,11 @@ static void V2Protocol_Command_LeaveISPMode(void)
 	Endpoint_ClearIN();
 }
 
+/** Handler for the CMD_PROGRAM_FLASH_ISP and CMD_PROGRAM_EEPROM_ISP commands, writing out bytes,
+ *  words or pages of data to the attached device.
+ *
+ *  \param V2Command  Issued V2 Protocol command byte from the host
+ */
 static void V2Protocol_Command_ProgramMemory(uint8_t V2Command)
 {
 	struct
@@ -270,7 +301,7 @@ static void V2Protocol_Command_ProgramMemory(uint8_t V2Command)
 		uint8_t  ProgrammingCommands[3];
 		uint8_t  PollValue1;
 		uint8_t  PollValue2;
-		uint8_t  ProgData[256];
+		uint8_t  ProgData[512];
 	} Write_Memory_Params;
 	
 	uint8_t* NextWriteByte = Write_Memory_Params.ProgData;
@@ -380,6 +411,11 @@ static void V2Protocol_Command_ProgramMemory(uint8_t V2Command)
 	Endpoint_ClearIN();
 }
 
+/** Handler for the CMD_READ_FLASH_ISP and CMD_READ_EEPROM_ISP commands, reading in bytes,
+ *  words or pages of data from the attached device.
+ *
+ *  \param V2Command  Issued V2 Protocol command byte from the host
+ */
 static void V2Protocol_Command_ReadMemory(uint8_t V2Command)
 {
 	struct
@@ -436,6 +472,7 @@ static void V2Protocol_Command_ReadMemory(uint8_t V2Command)
 	}
 }
 
+/** Handler for the CMD_CHI_ERASE_ISP command, clearing the target's FLASH memory. */
 static void V2Protocol_Command_ChipErase(void)
 {
 	struct
@@ -465,6 +502,11 @@ static void V2Protocol_Command_ChipErase(void)
 	Endpoint_ClearIN();
 }
 
+/** Handler for the CMD_READ_FUSE_ISP, CMD_READ_LOCK_ISP, CMD_READ_SIGNATURE_ISP and CMD_READ_OSCCAL commands,
+ *  reading the requested configuration byte from the device.
+ *
+ *  \param V2Command  Issued V2 Protocol command byte from the host
+ */
 static void V2Protocol_Command_ReadFuseLockSigOSCCAL(uint8_t V2Command)
 {
 	struct
@@ -490,6 +532,11 @@ static void V2Protocol_Command_ReadFuseLockSigOSCCAL(uint8_t V2Command)
 	Endpoint_ClearIN();
 }
 
+/** Handler for the CMD_WRITE_FUSE_ISP and CMD_WRITE_LOCK_ISP commands, writing the requested configuration
+ *  byte to the device.
+ *
+ *  \param V2Command  Issued V2 Protocol command byte from the host
+ */
 static void V2Protocol_Command_WriteFuseLock(uint8_t V2Command)
 {
 	struct
@@ -511,6 +558,7 @@ static void V2Protocol_Command_WriteFuseLock(uint8_t V2Command)
 	Endpoint_ClearIN();
 }
 
+/** Handler for the CMD_SPI_MULTI command, writing and reading arbitrary SPI data to and from the attached device. */
 static void V2Protocol_Command_SPIMulti(void)
 {
 	struct
diff --git a/Projects/Incomplete/AVRISP/Lib/V2Protocol.h b/Projects/Incomplete/AVRISP/Lib/V2Protocol.h
index b0f1f83c0f2f4e814f392505cfa71a8c66157c4c..5c8bd75132223101c64b1412b52e55174631cbcd 100644
--- a/Projects/Incomplete/AVRISP/Lib/V2Protocol.h
+++ b/Projects/Incomplete/AVRISP/Lib/V2Protocol.h
@@ -49,6 +49,7 @@
 		/** Programmer ID string, returned to the host during the CMD_SIGN_ON command processing */
 		#define PROGRAMMER_ID                   "AVRISP_MK2"
 		
+		/** Mask for the reading or writing of the high byte in a FLASH word when issuing a low-level programming command */
 		#define READ_WRITE_HIGH_BYTE_MASK       (1 << 3)
 
 		#define PROG_MODE_PAGED_WRITES_MASK     (1 << 0)
diff --git a/Projects/Incomplete/AVRISP/Lib/V2ProtocolParams.c b/Projects/Incomplete/AVRISP/Lib/V2ProtocolParams.c
index 61f4a88e6a081abe35928ad2a6b440b884e62f19..9914c085e5edaab3b46687ba8256b49eaddd8ec0 100644
--- a/Projects/Incomplete/AVRISP/Lib/V2ProtocolParams.c
+++ b/Projects/Incomplete/AVRISP/Lib/V2ProtocolParams.c
@@ -84,24 +84,21 @@ static ParameterItem_t ParameterTable[] =
 	};
 
 
+/** Loads saved non-volatile parameter values from the EEPROM into the parameter table, as needed. */
 void V2Params_LoadEEPROMParamValues(void)
 {
 	/* Target RESET line polarity is a non-volatile value, retrieve current parameter value from EEPROM */
 	V2Params_GetParamFromTable(PARAM_RESET_POLARITY)->ParamValue = eeprom_read_byte(&EEPROM_Rest_Polarity);
 }
 
-static ParameterItem_t* V2Params_GetParamFromTable(uint8_t ParamID)
-{
-	/* Find the parameter in the parameter table if present */
-	for (uint8_t TableIndex = 0; TableIndex < (sizeof(ParameterTable) / sizeof(ParameterTable[0])); TableIndex++)
-	{
-		if (ParamID == ParameterTable[TableIndex].ParamID)
-		  return &ParameterTable[TableIndex];
-	}
-	
-	return NULL;
-}
-
+/** Retrieves the host PC read/write privellages for a given parameter in the parameter table. This should
+ *  be called before calls to \ref V2Params_GetParameterValue() or \ref V2Params_SetParameterValue() when
+ *  getting or setting parameter values in response to requests from the host.
+ *
+ *  \param ParamID  Parameter ID whose privellages are to be retrieved from the table
+ *
+ *  \return Privellages for the requested parameter, as a mask of PARAM_PRIV_* masks
+ */ 
 uint8_t V2Params_GetParameterPrivellages(uint8_t ParamID)
 {
 	ParameterItem_t* ParamInfo = V2Params_GetParamFromTable(ParamID);
@@ -112,6 +109,12 @@ uint8_t V2Params_GetParameterPrivellages(uint8_t ParamID)
 	return ParamInfo->ParamPrivellages;
 }
 
+/** Retrieves the current value for a given parameter in the parameter table.
+ *
+ *  \param ParamID  Parameter ID whose value is to be retrieved from the table
+ *
+ *  \return Current value of the parameter in the table, or 0 if not found
+ */ 
 uint8_t V2Params_GetParameterValue(uint8_t ParamID)
 {
 	ParameterItem_t* ParamInfo = V2Params_GetParamFromTable(ParamID);
@@ -122,6 +125,13 @@ uint8_t V2Params_GetParameterValue(uint8_t ParamID)
 	return ParamInfo->ParamValue;
 }
 
+/** Sets the value for a given parameter in the parameter table.
+ *
+ *  \param ParamID  Parameter ID whose value is to be set in the table
+ *  \param Value  New value to set the parameter to
+ *
+ *  \return Pointer to the associated parameter information from the parameter table if found, NULL otherwise
+ */
 void V2Params_SetParameterValue(uint8_t ParamID, uint8_t Value)
 {
 	ParameterItem_t* ParamInfo = V2Params_GetParamFromTable(ParamID);
@@ -135,3 +145,22 @@ void V2Params_SetParameterValue(uint8_t ParamID, uint8_t Value)
 	if (ParamID == PARAM_RESET_POLARITY)
 	  eeprom_write_byte(&EEPROM_Rest_Polarity, Value);  
 }
+
+/** Retrieves a parameter entry (including ID, value and privellages) from the parameter table that matches the given
+ *  parameter ID.
+ *
+ *  \param ParamID  Parameter ID to find in the table
+ *
+ *  \return Pointer to the associated parameter information from the parameter table if found, NULL otherwise
+ */
+static ParameterItem_t* V2Params_GetParamFromTable(uint8_t ParamID)
+{
+	/* Find the parameter in the parameter table if present */
+	for (uint8_t TableIndex = 0; TableIndex < (sizeof(ParameterTable) / sizeof(ParameterTable[0])); TableIndex++)
+	{
+		if (ParamID == ParameterTable[TableIndex].ParamID)
+		  return &ParameterTable[TableIndex];
+	}
+	
+	return NULL;
+}
diff --git a/Projects/Incomplete/AVRISP/Lib/V2ProtocolParams.h b/Projects/Incomplete/AVRISP/Lib/V2ProtocolParams.h
index d0a467b00a514a34efe2467942278f1114e29b45..9c0f044c2449d54a0177456a19bed75ded81f7ee 100644
--- a/Projects/Incomplete/AVRISP/Lib/V2ProtocolParams.h
+++ b/Projects/Incomplete/AVRISP/Lib/V2ProtocolParams.h
@@ -46,10 +46,10 @@
 		#include "V2ProtocolConstants.h"
 
 	/* Macros: */
-		/* Parameter privellage mask to allow the host PC to read the parameter's value */
+		/** Parameter privellage mask to allow the host PC to read the parameter's value */
 		#define PARAM_PRIV_READ   (1 << 0)
 
-		/* Parameter privellage mask to allow the host PC to change the parameter's value */
+		/** Parameter privellage mask to allow the host PC to change the parameter's value */
 		#define PARAM_PRIV_WRITE  (1 << 1)
 
 	/* Type Defines: */
diff --git a/Projects/Incomplete/AVRISP/Lib/V2ProtocolTarget.c b/Projects/Incomplete/AVRISP/Lib/V2ProtocolTarget.c
index e23885bb39596597b3cccb296fbf7eb8106c8ff9..a39c5e96d1cda258143b568c883de5adc78ff249 100644
--- a/Projects/Incomplete/AVRISP/Lib/V2ProtocolTarget.c
+++ b/Projects/Incomplete/AVRISP/Lib/V2ProtocolTarget.c
@@ -36,20 +36,36 @@
 #include "V2ProtocolTarget.h"
 
 /** Current memory address for FLASH/EEPROM memory read/write commands */
-uint32_t CurrentAddress;	
+uint32_t CurrentAddress;
 
+/** Converts the given AVR Studio SCK duration parameter (set by a SET PARAM command from the host) to the nearest
+ *  possible SPI clock prescaler mask for passing to the SPI_Init() routine.
+ *
+ *  \return Nearest SPI prescaler mask for the given SCK frequency
+ */
 uint8_t V2Protocol_GetSPIPrescalerMask(void)
 {
 	static const uint8_t SPIMaskFromSCKDuration[TOTAL_PROGRAMMING_SPEEDS] =
 	{
-		#if (F_CPU == 8000000)
-		SPI_SPEED_FCPU_DIV_2,
-		#endif
-		SPI_SPEED_FCPU_DIV_2, SPI_SPEED_FCPU_DIV_4, SPI_SPEED_FCPU_DIV_8,
-		SPI_SPEED_FCPU_DIV_16, SPI_SPEED_FCPU_DIV_32, SPI_SPEED_FCPU_DIV_64
-		#if (F_CPU == 16000000)
-		, SPI_SPEED_FCPU_DIV_128
-		#endif
+	#if (F_CPU == 8000000)
+		SPI_SPEED_FCPU_DIV_2,    // AVRStudio =   8MHz SPI, Actual =   4MHz SPI
+		SPI_SPEED_FCPU_DIV_2,    // AVRStudio =   4MHz SPI, Actual =   4MHz SPI
+		SPI_SPEED_FCPU_DIV_4,    // AVRStudio =   2MHz SPI, Actual =   2MHz SPI
+		SPI_SPEED_FCPU_DIV_8,    // AVRStudio =   1MHz SPI, Actual =   1MHz SPI
+		SPI_SPEED_FCPU_DIV_16,   // AVRStudio = 500KHz SPI, Actual = 500KHz SPI
+		SPI_SPEED_FCPU_DIV_32,   // AVRStudio = 250KHz SPI, Actual = 250KHz SPI
+		SPI_SPEED_FCPU_DIV_64    // AVRStudio = 125KHz SPI, Actual = 125KHz SPI	
+	#if (F_CPU == 16000000)
+		SPI_SPEED_FCPU_DIV_2,    // AVRStudio =   8MHz SPI, Actual =   8MHz SPI
+		SPI_SPEED_FCPU_DIV_4,    // AVRStudio =   4MHz SPI, Actual =   4MHz SPI
+		SPI_SPEED_FCPU_DIV_8,    // AVRStudio =   2MHz SPI, Actual =   2MHz SPI
+		SPI_SPEED_FCPU_DIV_16,   // AVRStudio =   1MHz SPI, Actual =   1MHz SPI
+		SPI_SPEED_FCPU_DIV_32,   // AVRStudio = 500KHz SPI, Actual = 500KHz SPI
+		SPI_SPEED_FCPU_DIV_64,   // AVRStudio = 250KHz SPI, Actual = 250KHz SPI		
+		SPI_SPEED_FCPU_DIV_128   // AVRStudio = 125KHz SPI, Actual = 125KHz SPI
+	#else
+		#error No SPI prescaler masks for chosen F_CPU speed.
+	#endif
 	};
 
 	uint8_t SCKDuration = V2Params_GetParameterValue(PARAM_SCK_DURATION);
@@ -60,6 +76,11 @@ uint8_t V2Protocol_GetSPIPrescalerMask(void)
 	return SPIMaskFromSCKDuration[SCKDuration];
 }
 
+/** Asserts or deasserts the target's reset line, using the correct polarity as set by the host using a SET PARAM command.
+ *  When not asserted, the line is tristated so as not to intefere with normal device operation.
+ *
+ *  \param ResetTarget Boolean true when the target should be held in reset, false otherwise
+ */
 void V2Protocol_ChangeTargetResetLine(bool ResetTarget)
 {
 	if (ResetTarget)
@@ -76,6 +97,18 @@ void V2Protocol_ChangeTargetResetLine(bool ResetTarget)
 	}
 }
 
+/** Waits until the last issued target memory programming command has completed, via the check mode given and using
+ *  the given parameters.
+ *
+ *  \param ProgrammingMode  Programming mode used and completion check to use, a mask of PROG_MODE_* constants
+ *  \param PollAddress  Memory address to poll for completion if polling check mode used
+ *  \param PollValue  Poll value to check against if polling check mode used
+ *  \param DelayMS  Milliseconds to delay before returning if delay check mode used
+ *  \param ReadMemCommand  Device low-level READ MEMORY command to send if value check mode used
+ *
+ *  \return V2 Protocol status \ref STATUS_CMD_OK if the no timeout occurred, \ref STATUS_RDY_BSY_TOUT or
+ *          \ref STATUS_CMD_TOUT otherwise
+ */
 uint8_t V2Protocol_WaitForProgComplete(uint8_t ProgrammingMode, uint16_t PollAddress, uint8_t PollValue,
                                        uint8_t DelayMS, uint8_t ReadMemCommand)
 {
@@ -101,7 +134,7 @@ uint8_t V2Protocol_WaitForProgComplete(uint8_t ProgrammingMode, uint16_t PollAdd
 			while ((SPI_TransferByte(0x00) != PollValue) && (TCNT0 < TARGET_BUSY_TIMEOUT_MS));
 
 			if (TCNT0 >= TARGET_BUSY_TIMEOUT_MS)
-			 ProgrammingStatus = STATUS_RDY_BSY_TOUT;
+			 ProgrammingStatus = STATUS_CMD_TOUT;
 			
 			break;		
 		case PROG_MODE_WORD_READYBUSY_MASK:
@@ -113,6 +146,11 @@ uint8_t V2Protocol_WaitForProgComplete(uint8_t ProgrammingMode, uint16_t PollAdd
 	return ProgrammingStatus;
 }
 
+/** Waits until the target has completed the last operation, by continuously polling the device's
+ *  BUSY flag until it is cleared, or until the \ref TARGET_BUSY_TIMEOUT_MS timeout period has expired.
+ *
+ *  \return V2 Protocol status \ref STATUS_CMD_OK if the no timeout occurred, \ref STATUS_RDY_BSY_TOUT otherwise
+ */
 uint8_t V2Protocol_WaitWhileTargetBusy(void)
 {
 	TCNT0 = 0;
@@ -132,6 +170,10 @@ uint8_t V2Protocol_WaitWhileTargetBusy(void)
 	  return STATUS_CMD_OK;
 }
 
+/** Sends a low-level LOAD EXTENDED ADDRESS command to the target, for addressing of memory beyond the
+ *  64KB boundary. This sends the command with the correct address as indicated by the current address
+ *  pointer variable set by the host when a SET ADDRESS command is issued.
+ */
 void V2Protocol_LoadExtendedAddress(void)
 {
 	SPI_SendByte(0x4D);
diff --git a/Projects/Incomplete/AVRISP/Lib/V2ProtocolTarget.h b/Projects/Incomplete/AVRISP/Lib/V2ProtocolTarget.h
index 6dce59d6c9723d14d6c4ba7b871f15dded8586d6..1e0364d9ccfa77a2cc8eeb0b270ac0a0d12eb52f 100644
--- a/Projects/Incomplete/AVRISP/Lib/V2ProtocolTarget.h
+++ b/Projects/Incomplete/AVRISP/Lib/V2ProtocolTarget.h
@@ -58,10 +58,14 @@
 		extern uint32_t CurrentAddress;
 
 	/* Inline Functions: */
-		static inline void V2Protocol_DelayMS(uint8_t MS)
+		/** Blocking delay for a given number of milliseconds, via a hardware timer.
+		 *
+		 *  \param DelayMS  Number of milliseconds to delay for
+		 */
+		static inline void V2Protocol_DelayMS(uint8_t DelayMS)
 		{
 			TCNT0 = 0;
-			while (TCNT0 < MS);
+			while (TCNT0 < DelayMS);
 		}
 
 	/* Function Prototypes: */