Little status post here for those curious about the fringe of hacking this thing... last night I spent a few hours compiling/assembling (hardware/software), adjusting, tweaking, and actually successfully programming my Jalapeno using only an Arduino. I think this effectively lifts all limitations on what JTAG programmer you can use
I compiled 1.2.9 with some comment adjustments in the config code. As others have noted, the code seems to be haphazardly thrown together with huge swaths of code commented out (like, in my case, the routines to test chips on startup - commented out by default). It compiled in AVR Studio, then I took the HEX file and made a BIN out of it - then for the next 2.5 hours, the Arduino and the Jalapeno had a conversation with the help of UrJTAG and Ubuntu. Finally, when it moved on to verifying (and a few pages passed by without errors), I killed the program and rebooted the Jally.
It worked! Sort of. It boots up, lights up the 2 LEDs for the two chips, and responds to ID commands (ZCX, etc), indicating the new firmware is there. Chips now running at 300MHz, which is far more than I expect it to run at (but with poor commenting in the code, I couldn't tell what I was setting it to). But that's all it will do now. The moment I fire up a miner, the Jally knocks out one of the chip LEDs and goes into a hard-lock until I power-cycle it.
Not bad for the first guy flashing a Jally using only an Arduino and about 30% custom code made up on the spot (on both UrJTAG's source code and in Arduiggler's code). When I get back to it today I'll give it another go.
Damn shame the "set frequency factor" (ZVX + 0x04 + 4-byte code) command interpreter function is broken - always saying "INVALID DATA" no matter what it's given, probably due to a broken wait/timeout loop mechanism (killing the command entry too early like it does with Z*X commands if not copied/pasted all at once). Probably could use that command to get the firmware working as it is now