Do a clean Bootleg install with all of the mods on a vanilla FF7 for the first time.
Customize to your liking while keeping track.
Then you can remove most of the already installed mods, add new mods and run Bootleg without all the old baggage.
Bootleg should be much quicker on subsequent installs.
That first run through is very important.
Bootleg needs all those models from the installers like Remix.
If any files are mismatched, the game goes haywire.
EDIT:
Bootleg 0030 in ready for release later today.Bootleg 
Front 
End is now working with every Bootleg switch!
It's still missing many of the screenshots and the layout is terrible.
Does anyone want access to the BFE tech preview?  I'd appreciate any feedback on making things more visually appealing and easier to configure.  If I receive any requests, I'll release BFE as a separate download with the upcoming Bootleg release.
EDIT:
Bootleg 0030 is now available with BFE!BFE-- Bootleg Front End-- is a graphical front end interface for the Bootleg configurator.
New in 0030:
    Changed Version Numbering
    Added /I Switch to Install from Image
    Added /W Switch to Select Soundtrack
    Added bunny girls.rar
    Added sailor jupiter.rar
    Added sailor mars.rar
    Added Hi Res Sephiroth Model
    Added Cloud Carries Masamune
    Added Fixed Rebuilded Models: Man 11, Mr. Coates, Old Man 4, Punk 2, Punk 4, Sumo 1, Sumo 2, Wrestler 3
    Recovered Mike's Masamune Sword
    Recovered Kela51's Missing Ice Textures
    Updated Strayoff's Condor Minigame Mod
    Optimized Install Order
New Mod Downloads:
    bunny girls.rar       Aaiki14   Bunny Dress Field Models      Qhimm FILE
    sailor jupiter.rar    Aaiki14   Aeris Sailor Jupiter Model    Qhimm FILE
    sailor mars.rar       Aaiki14   Tifa Sailor Mars Model        Qhimm FILE-PitBrat