By adding stuff, i assume you mean you added a new screenpack in some way? Or parts of one. Most of mugen in 1.0 and up uses a coord space parameter to set scaling, it is possible you used one that doesn't match up with what you have, or is for winmugen, where the option screen was locked at 320x240.
Easy mode is simply replace mugen.cfg and system.def with the original ones. Hard mode is taking out exactly what you broke it with. If you were doing stuff file by file without testing each time, that's going to be awkward.
I recommend easy mode, that should take care of things quickly. Won't be as pretty, but will be fast. Back them up first so you can add values back.