So I just tried installing the XPLAINBridge mentioned https://www.avrfreaks.net/index.php?name=PNphpBB2&file=viewtopic&t=87393 and http://fourwalledcubicle.com/blog/archives/508
It compiled fine and I used a JTAG-MKII to program the flash with the hex file:
avrdude -p usb1287 -c jtag2 -P usb -e -U \ flash:w:XPLAINBridge.hex
And this step went fine. I disconnected the MKII and cycled the XPLAIN power. lsusb shows this (regardless if TCK is shorted to ground or not):
Bus 002 Device 036: ID 03eb:204b Atmel Corp.
In windows it shows up as the "Dean Camera LUDA XPLAIN Bridge" so I think the flash worked correctly? But it never shows up as an ISP-MKII clone like the blog mentions it should. It seems like I half working version.
The worst part is... JTAG no longer works so I can't even flash over the backup I made.
Any ideas as what I should try next?