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There are sites that track all the changes from reissue to reissue. I know the 90s Rhino reissue had different solo edits, outros and different overdubs, like ratchet on "Willie The Pimp". FZ made a lot of changes to the early records when he reissued them in the late 80s-early 90s on CD.
In general you want the 2012 releases of everything as they revert to the original vinyl mixes before Zappa swathed everything in reverb, rerecorded the bass/drums etc. The recent 6 cd set of the original sessions is also a lot of fun!