Other than needing to reboot my computer to change the parallel port into EPP mode (in the BIOS setup), I had no troubled getting it working. I'm using ucon64 2.0.1 from the cvs repo along with the front-end, uf. I found a bug right off in ucon64 - they have the byte swapping backwards in ttt_read_rom_w. It was easy to tell - just dump the flash cart the way it comes and look in a hex editor. The bytes of each word were clearly backwards. I flipped the routines and poof! Nice dump of the cart.

Anywho, between the -multi option code in ucon64 and my disassembly of the multi-loader, I've figured out how the flash and save ram bank selecting works. I'm not sure if this is supposed to be a secret, but I won't say anything until I get a few opinions here. I've not signed any NDA's, nor received any special info. I'm going from open source code and disassembly of a program with no restriction about RE in the license, so I don't see a problem with relaying any info.
I do have to say, it dumps the flash FAST. Even writing is pretty fast - it wrote a 512 KB cart image in about 5 to 6 seconds.