Hi Nick
When I connected the Mega to a Uno using pins 51, 52 and 53 I get this output
Atmega chip detector.
Entered programming mode OK.
Signature = 1E 98 01
Processor = ATmega2560
Flash memory size = 262144
LFuse = FF
HFuse = D8
EFuse = FD
Lock byte = FF
Clock calibration = 81
Bootloader in use: Yes
EEPROM preserved through erase: No
Watchdog timer always on: No
Bootloader is 8192 bytes starting at 3E000
Bootloader:
3E000: 0D 94 F6 F2 0D 94 1F F3 0D 94 1F F3 0D 94 1F F3
3E010: 0D 94 1F F3 0D 94 1F F3 0D 94 1F F3 0D 94 1F F3
3E020: 0D 94 1F F3 0D 94 1F F3 0D 94 1F F3 0D 94 1F F3
.....
3FFE0: FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF
3FFF0: FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF FF
MD5 sum of bootloader = 1E 35 14 08 1F 65 7F 8C 96 50 69 9F 19 1E 3D F0
First 256 bytes of program memory:
0: 0C 94 E3 71 0C 94 0F 72 0C 94 0F 72 0C 94 0F 72
10: 0C 94 0F 72 0C 94 0F 72 0C 94 0F 72 0C 94 0F 72
20: 0C 94 0F 72 0C 94 0F 72 0C 94 0F 72 0C 94 0F 72
30: 0C 94 0F 72 0C 94 0F 72 0C 94 0F 72 0C 94 0F 72
40: 0C 94 0F 72 0C 94 0F 72 0C 94 0F 72 0C 94 0F 72
50: 0C 94 1C 9F 0C 94 0F 72 0C 94 0F 72 0C 94 85 A3
60: 0C 94 0F 72 0C 94 B5 A6 0C 94 F9 A7 0C 94 0F 72
70: 0C 94 0F 72 0C 94 0F 72 0C 94 0F 72 0C 94 0F 72
80: 0C 94 0F 72 0C 94 0F 72 0C 94 0F 72 0C 94 0F 72
90: 0C 94 F5 A6 0C 94 38 A8 0C 94 0F 72 0C 94 0F 72
A0: 0C 94 0F 72 0C 94 0F 72 0C 94 0F 72 0C 94 0F 72
B0: 0C 94 0F 72 0C 94 0F 72 0C 94 0F 72 0C 94 0F 72
C0: 0C 94 0F 72 0C 94 0F 72 0C 94 0F 72 0C 94 35 A7
D0: 0C 94 77 A8 0C 94 0F 72 0C 94 75 A7 0C 94 B6 A8
E0: 0C 94 0F 72 05 A8 4C CD B2 D4 4E B9 38 36 A9 02
F0: 0C 50 B9 91 86 88 08 3C A6 AA AA 2A BE 00 00 00
Which appears to be as it should be.
There is an ISCP header near the USB socket but I have not been able to identify which pins to connect too. Using a continuity test I have been able to identify the GND and 5v, but not any of the others.
A close inspection of the ATmel8U2 chip seems to show some physical damage (The ATmel lettering is discoloured - I can upload a photo if required) so I suspect that this chip is fried.
Cheers