The first step is to just test the character/stage to see if it even needs anything done. If it does, it will helpfully generate an error message and you'll know where to start. More often than not, you won't have to do anything, but there's always some bullshit that manages to crop up. You won't have to do anything different than you would for Mugen 1.0.
Badly written displaytoclipboard states = just null them out
Usage of Z values in velocity = go to the effort of tediously removing them
Corrupted graphics for the select icon or other sprites = use CharSffDtoW.exe
Helpful thing for testing:
Open a file in notepad and paste this in there:
"mugen.exe" "%p1%" "%p2%" -s %st% -p2.ai 0 -p2.color 1
Save it into your mugen folder as something like "testcharacter.bat". It has to be a .BAT file. Not .bat.txt. Hopefully it's obviously how this works. This is just an example, so you need to set the parameters to characters and a stage that you actually have (or want to test). I like to use cvsryu as my standard for testing, so I always use him as p2 in my typical testing environment. If you don't have cvsryu, get him, or change that value. If you have a new character to test, change p1 to that character (from kfm). And if/when you want to test a stage, change the st value from kfm to the new stage. If the stage's DEF is blablabroken.def, you only need the blablabroken part.
To edit the file after you saved it, right click on it and choose edit.