God this is a mess, I'd rather have you work with this instead since it's a little less confusing. Also try using 1.0 now, it's the most used by now.
Download this and drop the "EveBattle" folder into the data folder
Open up your mugen.cfg (It's in data) with notepad and find the motif line, and then change it so reads as
motif = data/EveBattle/system.def
This will give you the category select
If you want to use the normal select instead of the category list then make sure it reads as
motif = data/EveBattle/EVEvolve/system.def
This will give you the standard select, make sure you edit the select file inside "EvEvolve" if you're using this one.
That should be it, sorry for the late reply.
One more thing if you're using 1.0, open up the mugen.cfg again and head down to the
[Config] section, it's under [Rules] and change the gamewidth and gameheight to this
GameWidth = 640
GameHeight = 480