My Hacked Rom crashes...will EXPLAIN

Is it preferable I do the cosmetic edits with FF3USME before or after I patch the rom or roms?

You should be able to do them before and after applying the patches if they work correctly unless I'm mistaken. Maybe Poco Loco could give you more in about his weapon patch and what does it change exactly. It's the only thing I'm totally ignorant about.

I use a Final Fantasy III Version 1.1 rom for hacking the game, if you know where I can find a headerless rom for the game, it'd be appreciated if I can't find the issue I am having.

There are small differences between version 1.0 and 1.1 but I don't know exactly what they are. You should also find out if your patches require a headered ROM or not, and that should be said in the documentation that comes with the patch, if there is any... To see if your ROM has a header, open a Hex editor and if the 200 first bytes are 00 (except the first few) then you have a header. They are some tools available to remove or apply a header if you can't do it manually. I can point you out to a FF3us ROM 1.0 with header in a PM.