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I have a 2006 convertible and am having problems with the top. I really don't want to take back to the dealer unless I have to. I usually do most of my work myself unless it is a major repair because it seems my vehicles oftentimes come back with more problems than they had when they went to the service department for warranty work. It is the manual top, and the problems have existed since the car came in about two weeks ago. First of all, the top is difficult to latch . . . the pin (mounted on the convertible top part) on the passenger's side misses the hole that it latches in above the windshield by about 3/16", the driver's side aligns perfectly. You have to use a lot of force to get the top to go into the hole and latch. I have looked and only see an adjustment to adjust the latch up and down, not left to right. It appears the latch needs to be adjusted slightly toward the center of the car. Any help would be appreciated. Also, when lowering the top, you must first raise the front portion of the top, to release the rear portion. In the process of doing this, there is a rail that hits the rear cover behind the waterfall. The rail had a self-adhesive cushion on each side, but they were applied about 1" too high from the factory. Therefore, the first day I brought the car home, it had already started chipping the fiberglass. I removed the cushions and re-appled them in the correct place. (I am still wondering if anyone else's manual top hits like mine when you raise up on the front part of the top . . . if they do not / are not supposed to hit, what adjustments should me made?)
It looks like you definitely have problems with the top fit. I strongly suggest you take it back to your dealer to have their body shop look it over. If you really don't like the dealers service dept. check around your area for another one with a good reputation. The thing you must do is politely explain your concerns about someone working on the car as well as the problem to the service manager. If possible ask to talk to the technician who will do the work so you can personally show them what the problem is.
Ken has had a C6 with the manual top but is out of the store untill later this week sometime. It's possible he may be able to help you, I would put a post to him under Kens Newsletters here on the forum.