do the 07's have the auto up on both driver and passenger windows? my moms altima (i know its not a mustang) had a similar problem. if you used the auto up then it would go all the way up and then come back down like 5-6 inches. if you just used the regular up then you could close it properly. try this and see if it works. i know its not a permanent fix, but it should help you out for the time being. as far as fixing it goes, it seems like the window might be going up too high and hitting a stop and making it go back down a few inches. make sure the window is adjusted properly. also, you might want to check in the s197 tech section, as the convertible section doesnt get too much traffic.
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1994 Mustang GT, just a few minor appearance mods, engine mostly stock (for now)
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