When I removed all the files from my card last night, extracted the new EDFC folder, copied my saves, then my ROMs, I got the "default settings" prompt, then it hung up. On a reset/power up, I also got stuck at "OS Init". However, I then took the EDFC folder, extracted it on my desktop, renamed it to "EDFC1", and copied it over. I then copied in my saves, deleted the old EDFC folder, and renamed the "EDFC1" to "EDFC". That seemed to do the trick. I have no idea why that's the case, because I've had to do weird stuff like this each time I've upgraded, but I eventually get it to take.
Also note that when I did this, I did not recopy my ROMs like I had before, I left everything in the state it was from the first attempt at installing.
Is it possible that the FPGA is somehow retaining the location of the previous EDFC folder on the memory card, and gets goofy if it ends up in the same spot (or near it) on the card? And when it fails (or is effectively forced to move like I did above), that it picks up on the location change and parses it in correctly? Just spitballing here, I have no idea.