After looking at the actual error I was able to fix the error by simply adding a new end code to the Lua script. I got the following output from the script
// File = chAudioBoot_ATMEGA168_IN_PD1_LED_PB5.hex// Loader start: 3C00, length: 1024
// MD5 sum = 86 9B DA 86 0E 68 2B F1 0C 20 E5 47 D8 3C 8D E5
byte PROGMEM chAudioBoot_ATMEGA168_IN_PD1_LED_PB5_hex [] = {
0x0C, 0x94, 0x34, 0x1E, 0x0C, 0x94, 0x51, 0x1E, 0x0C, 0x94, 0x51, 0x1E, 0x0C, 0x94, 0x51, 0x1E,
0x0C, 0x94, 0x51, 0x1E, 0x0C, 0x94, 0x51, 0x1E, 0x0C, 0x94, 0x51, 0x1E, 0x0C, 0x94, 0x51, 0x1E,
0x0C, 0x94, 0x51, 0x1E, 0x0C, 0x94, 0x51, 0x1E, 0x0C, 0x94, 0x51, 0x1E, 0x0C, 0x94, 0x51, 0x1E,
0x0C, 0x94, 0x51, 0x1E, 0x0C, 0x94, 0x51, 0x1E, 0x0C, 0x94, 0x51, 0x1E, 0x0C, 0x94, 0x51, 0x1E,
0x0C, 0x94, 0x51, 0x1E, 0x0C, 0x94, 0x51, 0x1E, 0x0C, 0x94, 0x51, 0x1E, 0x0C, 0x94, 0x51, 0x1E,
0x0C, 0x94, 0x51, 0x1E, 0x0C, 0x94, 0x51, 0x1E, 0x0C, 0x94, 0x51, 0x1E, 0x0C, 0x94, 0x51, 0x1E,
0x0C, 0x94, 0x51, 0x1E, 0x0C, 0x94, 0x51, 0x1E, 0x11, 0x24, 0x1F, 0xBE, 0xCF, 0xEF, 0xD4, 0xE0,
0xDE, 0xBF, 0xCD, 0xBF, 0x11, 0xE0, 0xA0, 0xE0, 0xB1, 0xE0, 0xE8, 0xE9, 0xFF, 0xE3, 0x02, 0xC0,
0x05, 0x90, 0x0D, 0x92, 0xA0, 0x30, 0xB1, 0x07, 0xD9, 0xF7, 0x11, 0xE0, 0xA0, 0xE0, 0xB1, 0xE0,
0x01, 0xC0, 0x1D, 0x92, 0xA5, 0x38, 0xB1, 0x07, 0xE1, 0xF7, 0x0E, 0x94, 0xC3, 0x1F, 0x0C, 0x94,
0xCA, 0x1F, 0x0C, 0x94, 0x00, 0x1E, 0xDF, 0x93, 0xCF, 0x93, 0x00, 0xD0, 0x00, 0xD0, 0xCD, 0xB7,
0xDE, 0xB7, 0x1A, 0x82, 0x19, 0x82, 0x1A, 0x82, 0x19, 0x82, 0x89, 0xB1, 0x82, 0x70, 0x28, 0x2F,
0x30, 0xE0, 0x89, 0xB1, 0x90, 0xE0, 0x82, 0x70, 0x90, 0x70, 0x28, 0x17, 0x39, 0x07, 0xC9, 0xF3,
0x69, 0xB1, 0x62, 0x70, 0x10, 0x92, 0xB2, 0x00, 0x40, 0xE0, 0x50, 0xE0, 0x89, 0xB1, 0x26, 0x2F,
0x30, 0xE0, 0x90, 0xE0, 0x82, 0x70, 0x90, 0x70, 0x28, 0x17, 0x39, 0x07, 0xB9, 0xF3, 0x20, 0x91,
0xB2, 0x00, 0x10, 0x92, 0xB2, 0x00, 0x69, 0xB1, 0x62, 0x70, 0x48, 0x30, 0x51, 0x05, 0x30, 0xF0,
0x89, 0x81, 0x9A, 0x81, 0x82, 0x0F, 0x91, 0x1D, 0x9A, 0x83, 0x89, 0x83, 0x4F, 0x5F, 0x5F, 0x4F,
0x40, 0x31, 0x51, 0x05, 0x19, 0xF7, 0x29, 0x81, 0x3A, 0x81, 0xC9, 0x01, 0x88, 0x0F, 0x99, 0x1F,
0x82, 0x0F, 0x93, 0x1F, 0x25, 0xE0, 0x96, 0x95, 0x87, 0x95, 0x2A, 0x95, 0xE1, 0xF7, 0x9C, 0x83,
0x8B, 0x83, 0x80, 0x91, 0xB2, 0x00, 0x2B, 0x81, 0x3C, 0x81, 0x90, 0xE0, 0x82, 0x17, 0x93, 0x07,
0xC0, 0xF3, 0x16, 0xC0, 0x89, 0xB1, 0x90, 0xE0, 0x82, 0x70, 0x90, 0x70, 0x28, 0x17, 0x39, 0x07,
0xC9, 0xF3, 0x49, 0xB1, 0x10, 0x92, 0xB2, 0x00, 0x80, 0x91, 0xB2, 0x00, 0x2B, 0x81, 0x3C, 0x81,
0x90, 0xE0, 0x82, 0x17, 0x93, 0x07, 0xC0, 0xF3, 0x64, 0x2F, 0x62, 0x70, 0x10, 0x92, 0xB2, 0x00,
0x26, 0x2F, 0x30, 0xE0, 0x89, 0xB1, 0x90, 0xE0, 0x82, 0x70, 0x90, 0x70, 0x28, 0x17, 0x39, 0x07,
0x09, 0xF3, 0x49, 0xB1, 0x42, 0x70, 0x58, 0xE0, 0xA0, 0xE0, 0x60, 0xE0, 0x70, 0xE0, 0x89, 0xB1,
0x24, 0x2F, 0x30, 0xE0, 0x90, 0xE0, 0x82, 0x70, 0x90, 0x70, 0x28, 0x17, 0x39, 0x07, 0xB9, 0xF3,
0x10, 0x92, 0xB2, 0x00, 0x49, 0xB1, 0x80, 0x91, 0xB2, 0x00, 0x2B, 0x81, 0x3C, 0x81, 0x90, 0xE0,
0x82, 0x17, 0x93, 0x07, 0xC0, 0xF3, 0x29, 0xB1, 0x22, 0x70, 0xEA, 0x2F, 0xF0, 0xE0, 0xE0, 0x50,
0xFF, 0x4F, 0x80, 0x81, 0x88, 0x0F, 0x80, 0x83, 0x42, 0x70, 0x42, 0x17, 0x11, 0xF0, 0x81, 0x60,
0x80, 0x83, 0x51, 0x50, 0x11, 0xF4, 0xAF, 0x5F, 0x58, 0xE0, 0x6F, 0x5F, 0x7F, 0x4F, 0x42, 0x2F,
0x24, 0xE0, 0x68, 0x32, 0x72, 0x07, 0x99, 0xF6, 0x30, 0xE0, 0x90, 0x91, 0x04, 0x01, 0x80, 0xE0,
0x20, 0x91, 0x03, 0x01, 0x82, 0x0F, 0x91, 0x1D, 0x8A, 0x5A, 0x95, 0x45, 0x09, 0xF4, 0x31, 0xE0,
0x83, 0x2F, 0x0F, 0x90, 0x0F, 0x90, 0x0F, 0x90, 0x0F, 0x90, 0xCF, 0x91, 0xDF, 0x91, 0x08, 0x95,
0x1F, 0x93, 0xCF, 0x93, 0xDF, 0x93, 0xDA, 0x01, 0xF8, 0x94, 0x83, 0xE0, 0xFB, 0x01, 0x80, 0x93,
0x57, 0x00, 0xE8, 0x95, 0x07, 0xB6, 0x00, 0xFC, 0xFD, 0xCF, 0xAB, 0x01, 0x11, 0xE0, 0xEB, 0x01,
0xC0, 0x58, 0xDF, 0x4F, 0x8C, 0x91, 0x11, 0x96, 0x3C, 0x91, 0x11, 0x97, 0x20, 0xE0, 0xF9, 0x01,
0xE8, 0x0F, 0xF1, 0x1D, 0xCF, 0x01, 0x12, 0x96, 0x0C, 0x01, 0xFA, 0x01, 0x10, 0x93, 0x57, 0x00,
0xE8, 0x95, 0x11, 0x24, 0x07, 0xB6, 0x00, 0xFC, 0xFD, 0xCF, 0x4E, 0x5F, 0x5F, 0x4F, 0x4C, 0x17,
0x5D, 0x07, 0x41, 0xF7, 0x85, 0xE0, 0xFB, 0x01, 0x80, 0x93, 0x57, 0x00, 0xE8, 0x95, 0x07, 0xB6,
0x00, 0xFC, 0xFD, 0xCF, 0x81, 0xE1, 0x80, 0x93, 0x57, 0x00, 0xE8, 0x95, 0xDF, 0x91, 0xCF, 0x91,
0x1F, 0x91, 0x08, 0x95, 0x82, 0xE0, 0x80, 0x93, 0xB1, 0x00, 0x08, 0x95, 0x14, 0xB8, 0x17, 0xB8,
0x1A, 0xB8, 0xF8, 0x94, 0x10, 0x92, 0xB1, 0x00, 0xEE, 0x27, 0xFF, 0x27, 0x09, 0x94, 0x08, 0x95,
0xFF, 0x92, 0x0F, 0x93, 0x1F, 0x93, 0xCF, 0x93, 0xDF, 0x93, 0x82, 0xE0, 0x80, 0x93, 0xB1, 0x00,
0xC0, 0xE1, 0xD7, 0xE2, 0x66, 0xE0, 0x53, 0xE0, 0x70, 0xE2, 0x80, 0x91, 0xB2, 0x00, 0x85, 0x36,
0xA8, 0xF0, 0x10, 0x92, 0xB2, 0x00, 0x21, 0x97, 0x89, 0xF4, 0x85, 0xB1, 0x87, 0x27, 0x85, 0xB9,
0x61, 0x50, 0x51, 0xF4, 0x2D, 0x98, 0x14, 0xB8, 0x17, 0xB8, 0x1A, 0xB8, 0xF8, 0x94, 0x10, 0x92,
0xB1, 0x00, 0xEE, 0x27, 0xFF, 0x27, 0x09, 0x94, 0xC0, 0xE1, 0xD7, 0xE2, 0x89, 0xB1, 0x24, 0x2F,
0x30, 0xE0, 0x90, 0xE0, 0x82, 0x70, 0x90, 0x70, 0x28, 0x17, 0x39, 0x07, 0x19, 0xF0, 0x49, 0xB1,
0x42, 0x70, 0x51, 0x50, 0x55, 0x23, 0xC9, 0xF6, 0x2D, 0x9A, 0x60, 0xE2, 0xF6, 0x2E, 0x0E, 0x94,
0x53, 0x1E, 0x88, 0x23, 0x79, 0xF4, 0x90, 0xE2, 0x80, 0x91, 0xB2, 0x00, 0x85, 0x36, 0xE0, 0xF3,
0x10, 0x92, 0xB2, 0x00, 0x21, 0x97, 0xC1, 0xF7, 0x85, 0xB1, 0x89, 0x27, 0x85, 0xB9, 0xC8, 0xEE,
0xD3, 0xE0, 0xF2, 0xCF, 0x85, 0xB1, 0x8F, 0x25, 0x85, 0xB9, 0x80, 0x91, 0x00, 0x01, 0x82, 0x30,
0x61, 0xF0, 0x83, 0x30, 0xE9, 0xF4, 0x14, 0xB8, 0x17, 0xB8, 0x1A, 0xB8, 0xF8, 0x94, 0x10, 0x92,
0xB1, 0x00, 0xEE, 0x27, 0xFF, 0x27, 0x09, 0x94, 0x13, 0xC0, 0x10, 0x91, 0x02, 0x01, 0x00, 0xE0,
0x80, 0x91, 0x01, 0x01, 0xB8, 0x01, 0x68, 0x0F, 0x71, 0x1D, 0x76, 0x95, 0x76, 0x2F, 0x66, 0x27,
0x77, 0x95, 0x67, 0x95, 0x80, 0xE0, 0x90, 0xE0, 0x45, 0xE0, 0x51, 0xE0, 0x0E, 0x94, 0x08, 0x1F,
0x10, 0x92, 0x00, 0x01, 0xC4, 0xCF, 0x25, 0x9A, 0x59, 0x9A, 0x0E, 0x94, 0x50, 0x1F, 0x80, 0xE0,
0x90, 0xE0, 0x08, 0x95, 0xF8, 0x94, 0xFF, 0xCF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
}; // end of chAudioBoot_ATMEGA168_IN_PD1_LED_PB5_hex
I then added that as a .h file into your Atmega_Board_Programmer and edited the code a bit to incorporate the Audioino Bootloader and I was able to successfully bootload a ATMEGA328p.
You can see the some of the alterations I made to the script and the output from Nick's programmer software in the screenshot:
http://cl.ly/image/2A2A0q333S0z
I have yet to actually test the bootloader however, so that would be the next step!