ROMs -- they are patched and altered from stock ROMs, Get your original copies back. Sure they probably will work in an emulator, will take 99.9% of ROM patches and if I was really bored I could probably even figure out a way to reverse it.
Saves.
They are in the saver folder on the miniSD. Do note that you will need to have the new one written back, personally I favour turning the game off, watching it write back and then loading a different game just to make sure things do not happen on the return journey.
Anyway in VBA click file -> import -> battery save. Same but use export -> to get the save out of there. Naturally you do need to save as you would in a normal game (some people seem to want savestates to work).
You may need to trim or pad out the save as the emulator or EZ4 may use a slightly different size to what it expects. For forum searchers this can work if you have a 3 in 1, however some loaders like AKAIO have an extra header on the file to allow it to manage things easier. You need to get rid of this for it to work on non AKAIO stuff.