There may not be any secrets in here for MUGEN creators, but for those just getting into MUGEN... this may help.
What you'll need:
Fighter Factory by VirtuallTek
Gimp (or any other image editor) [gimp is comparable to photoshop and completely free]
ALWAYS MAKE A BACKUP COPY BEFORE EDITING ANY FILES AS COULD RESULT IN UNDESIRED FRUSTRATION
1. Adding missing portraits/Aligning portraits
2. Increasing character limit in your screenpack/hiding characters off screen
3. Adding your own custom music to screenpack/stages
This is what I did for my current screenpack, I went through all characters visible on screen and kept the same theme for the small portraits (i still have to do all the large portraits ones to match each other). All small portraits "face off" in a marvel/MK vs DC/World. Every character's portrait was replaced that wasn't fitting my theme (a 25*25 crop of the character facing left (marvel/MK) or right (DC/World). I think it really creates the "full game" polish as if you don't edit the portraits your screenpack looks sloppy.
Here is what it looks like:
Well that's all I got for now folks... I will add to this later. I have at lease one more full section almost complete on character custom intros/win/fatalities/etc and how to make them work with other characters you have. But for now I have to get some sleep before work tomorrow. Feel free to open a discussion on your tips to get the most of out of your MUGEN. Your feedback/suggestions are always welcome here.