Ok, so I stripped off the Ebay ATmega128, and replaced it with a sparkfun-sourced ATmega2561. Immediately, first try, the bootloader flashes onto the chip. (and I hand-soldered the sucker too, so this was not guaranteed!)
Now, I'm working on getting communications going via the USB controller. I'm using a CP2102 controller, and the bootloader was configured for Megacore ATmega2561, 4.3v brown-out detection, LTO disabled, 16Mhz external crystal.
The following is what I get when trying to upload a sketch via USB:
Sketch uses 12,080 bytes (4%) of program storage space. Maximum is 261,120 bytes.
Global variables use 1,364 bytes (16%) of dynamic memory, leaving 6,828 bytes for local variables. Maximum is 8,192 bytes.
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 1 of 10: not in sync: resp=0x54
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 2 of 10: not in sync: resp=0x54
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 3 of 10: not in sync: resp=0x54
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 4 of 10: not in sync: resp=0x54
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 5 of 10: not in sync: resp=0x54
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 6 of 10: not in sync: resp=0x54
Problem uploading to board. See http://www.arduino.cc/en/Guide/Troubleshooting#upload for suggestions.
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 7 of 10: not in sync: resp=0x54
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 8 of 10: not in sync: resp=0x54
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 9 of 10: not in sync: resp=0x54
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 10 of 10: not in sync: resp=0x54
the sketch is actually in the Megacore examples folder, for the SD cardinfo sketch.
Anyone got anything I can try for this problem?