Sounds like a header issue (you either assembled with the header parameter to a non-headered rom, or assembled without the header parameter to a headered rom). The only two options are to replace the broken code/data, or start over.

That file I gave you was made specifically for FF6, and was not to be touched. It worked fine the way I gave it to you, with the exception of the header parameter. If your rom has a header, add the header parameter. If not, remove or comment out the header parameter. Run, assemble, boom. Screwing this part up will create problems.

Now, since you've already assembled on it, what you do to that specific rom no longer matters. You will either have to find and replace the broken code, or start over. The tutorial mentions the tracer, which is extremely helpful for this task. I'd suggest running WindHex32, compare your rom to a clean rom, and find out where things went wonky in the first bank (first 0xFFFF bytes).

There is also one other thing I did not realize when you said it. You said you used FF3usME to expand the rom to 4 megs, which is ok. But, if you moved the AI data or anything else after that, then I believe that will clash with this code, causing crashes.