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Do the mustang pup covers fit over most single coil sized pups? could i get for example http://www.guitarfetish.com/70k-True-Coil-_p_1966.html and remove the covers included and put a mustang pup cover on it? I'm not sure if i want to use the MIJ RI pickups for my project or try and get something else. I want to be able ot have the looks of the normal mustang pup covers.. Also is it possible to put a mustang pup cover over a SD hot rails/single sized HB pup?

I'm sure Mustang pups (the bobbin) are the same dimensions as Strat pups but obviously you would want flat pole pieces or the cover wont sit tight and could cause microphonic feedback. You could get this problem with Rails too, that is if the cover will even fit.
Might be worth googling the dimensions of traditional Fender pups, because some brands vary slightly and im not sure if GFS stuff is exactly the same.

You shouldn't have any trouble putting mustang covers on standard-sized strat pickups (Fender strat and mustang pickups are made of parts that are the same size). The cover should sit fine, but if you do have excessive vibration because of the polepiece pattern, you could use some foam matting tape on the top of the pickup to reduce vibration between the polepieces and the cover. An unstaggered set of strat pickups would most likely sit under the pickup cover a little better, but you should be fine either way.