No, you do not have to change the top mechanism. However, if you get an aftermarket window and you have a Ford factory top, you will have to get the zipper changed as they do not match. I use to sell Mustang parts and ran into this a lot. Kee Tops will sell you a rear glass that has a factory style zipper in it. It costs a little more but, it is worth the extra cost to not have to deal with all the headaches and the added expense of having to have the zipper replaced. There is also a manual available from Mustangs Unlimited, 5.0resto, Dallas Mustang that details all about the top. I suggest that you get this as it will provide you with a lot of useful imformation about your car. It has how to adjust the top, windows as well as installing a new top.
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