If I were you, I would get it fixed right. It will help your vehicle keep its value.
Yeah original manufacturer parts cost a lot, but quality wise they are ALWAYS better than an aftermarket part from what I have seen. I do work at a volkswagen/audi dealership.
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actually, vw/audi is one of the few where this is true. i've installed aftermarket cats a looonnnnnnnggggg time ago on vw's.....and they always came back witrh a cat. efficiency code. when i get them now, i go right to my local vw dealer for em.
as for the reason to use the factory parts on the top........mustangs have historically been built as coupes, and then shipped to an aftermarket company to convert it to a convertible. i think kar kraft does or did them.
because of this, they've had a tendency to rattle, and flex a lot. the added bracing wasn't really enough.
i'm not sure if the mustang convertibles are still built like that or if they're constructed as a convertible right off the bat now.........even if it is, it's still a uni-body, it's still based somewhat on the "fox" chassis, and it still flexes.
this is the most important reason to have the O.E. top on it. and preferably installed by the dealer, as they'll know this car in this area better than most of us non-dealer types will get the opportunity to.