Back onto here with my results. Here's the deal.
The FirmTek 5.1.3 updater contains a file called ROMFILE.1S2. It looks like it's compressed or something as trag pointed out. That's because somehow during the boot process, Mac OS X extracts two compressed kexts from it and installs them into /System/Library/Caches/com.apple.romextensions. However, it *is* the firmware file that needs to flashed onto the chip. No weird encodings, weird data line hookups, or anything like that.
The FirmTek updater will only update a card that already has FirmTek firmware on it, because it checks to see if its own driver is associated with the card. The WiebeTech updater can fail because it doesn't support all of the chips that FirmTek used. It may be possible, given a copy of the two kexts, to manually load them when a card has blank firmware and then get the FirmTek updater to work. Initial experimentation with that was successful for me...but you need the kext files first, so it's kind of a catch-22 unless you can figure out how to extract them from the firmware file or get them from someone else.
Silicon Image's DOS-based UPDFLASH.EXE utility seems to do the trick when booted from a FreeDOS boot floppy, but it is notoriously unreliable. I don't trust it. But if you give it enough tries, it should succeed. I had a TON of problems trying to run it direct from Windows 98 DOS mode though. I'd stick with the FreeDOS floppy. I would also make sure to put the firmware into it as a 256 KB file padded with 0xFF bytes at the end to make it a power of two. It appears maybe UPDFLASH won't correctly flash the end of the file otherwise.
Most importantly: the FirmTek firmware checks the ID of the flash chip on the card. It has a whitelist of allowed flash chips. If it's not a PMC Pm39LV040 or a Macronix MX29LV040, it won't load. There may be other possible chips, but I found the IDs of those two for sure, and I know the SST39VF040 is not supported.
The FirmTek 5.1.3 updater contains a file called ROMFILE.1S2. It looks like it's compressed or something as trag pointed out. That's because somehow during the boot process, Mac OS X extracts two compressed kexts from it and installs them into /System/Library/Caches/com.apple.romextensions. However, it *is* the firmware file that needs to flashed onto the chip. No weird encodings, weird data line hookups, or anything like that.
The FirmTek updater will only update a card that already has FirmTek firmware on it, because it checks to see if its own driver is associated with the card. The WiebeTech updater can fail because it doesn't support all of the chips that FirmTek used. It may be possible, given a copy of the two kexts, to manually load them when a card has blank firmware and then get the FirmTek updater to work. Initial experimentation with that was successful for me...but you need the kext files first, so it's kind of a catch-22 unless you can figure out how to extract them from the firmware file or get them from someone else.
Silicon Image's DOS-based UPDFLASH.EXE utility seems to do the trick when booted from a FreeDOS boot floppy, but it is notoriously unreliable. I don't trust it. But if you give it enough tries, it should succeed. I had a TON of problems trying to run it direct from Windows 98 DOS mode though. I'd stick with the FreeDOS floppy. I would also make sure to put the firmware into it as a 256 KB file padded with 0xFF bytes at the end to make it a power of two. It appears maybe UPDFLASH won't correctly flash the end of the file otherwise.
Most importantly: the FirmTek firmware checks the ID of the flash chip on the card. It has a whitelist of allowed flash chips. If it's not a PMC Pm39LV040 or a Macronix MX29LV040, it won't load. There may be other possible chips, but I found the IDs of those two for sure, and I know the SST39VF040 is not supported.