Hmmm, I didn't actually check for inconsistancies, better double check that.
Did you cut the tracks on the cart? I took a picture of another piece that I was going to wire up, but never did.
Also, its hard to cut tracks without sliding and cutting up another one, that you didn't mean to cut. I highly recommend an exacto knife, or razorblade. You can also hold the PCB up to a bright light and see the dark spots, to make sure the tracks were cut.
Your problem sounds like an address line may be stuck high or low. I haven't looked at it under an emulator, to see what banks are switching. To find that out, just run FF2E under an emulator, and watch points 0x8000 and 0xC000 to see when the switch (I think MMC1 switches 16K banks at those locations, but i could be wrong).