http://www.lukpac.org/~handmade/patio/vinylvscds/200motels.html This is pretty much all the info you'd need on it. I picked up the CDs just a few days ago in the local record store (Used, 29$ and its been OOP since 2002)
From what info you can find in that link it looks like the CD and official Vinyl were both taken from the same TWO TRACK masters that zappa sent to north america for the vinyl pressings. So basically this stuff can't possibly sound any better UNLESS the multi-track tapes are recovered and remastered. Apparently zappa didn't have the rights to re-release it or something so i guess we will just have to wait and see if the ZFT tries to do anything about it.
I've been listening to it for the past few nights and i'm really enjoying it. I actually kinda like the primitive two track sound, it has a certain charm. But a remaster with the muti-track tapes would sound awesome.