Sorry about the delay, I've been swamped with other projects.
I'm still unable to find any documentation on JTAG firmware or bootloader for SD2SNES. I'm quite familiar with JTAG flashing and willing to try both, I just need documentation for the SD2SNES.
EDIT: My USB flasher should work. I just need to verify pinouts are the same. I'm still unclear what procedure to follow for SD2SNES/Altera. I'm also not seeing the bootloader file anywhere, only firmwares.