Hello all I am having major problems modding !! Please help .

What do you mean by switch spell positions? Are you talking about manually recreating every spell in a new order in FF3usME? If so, this won't cause any other problems with your game. Even if you totally botched up the spells, only the spells you wrote on would be affected. This wouldn't cause any of the problems you mentioned above. Like Mad said, it sounds like you applied a patch that called for a ROM that's headered if yours isn't or unheadered if yours is. That's normally the cause of random stuff like that... Unless you have been making hex changes you aren't telling us about.