I'm working on a project, and my AVRISP died an untimely death. The only programmer I was able to borrow on short notice is a JTAGICE mk II, and I can't seem to find a Mega bootloader binary or instructions on how to burn it using the JTAGICE. The Arduino IDE won't talk to it. Anyone got any good suggestions?
The Arduino IDE won't talk to it
Not surprised as JTAG is an entirely different thing. You can use JTAG but it is a totally different command set. Se section 30.9 of the ATmega640/1280/1281/2560/2561 data sheet.
However, I have not seen anyone who has done this and written it up.