what year do you have? you should be able to change jus the back window, but if you have the top off and you gonna put a new back on you might as well do the top too the new mustangs have a one piece tops.
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95' GT blk/blk drop top
cai, 3:73, V force muffs, MGW shifter, jus added o/r h-pipe........for now
for the 94-04 you can change just the back window part if you want. but you are basically going to have the whole rest of the top off to do that. so while you are doing the back window, you might as well do the rest of the top too. if you dont then it prob isnt going to match colors and then a few years down the road you are going to have a worn out top, and nice back window.
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1994 Mustang GT, just a few minor appearance mods, engine mostly stock (for now)