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I have a 05 Z51 with a Lingenfelter 500hp make-over. Love everything about the car except that the glass top squeeks and rattles when driven over anything but absolutely smooth roads. The dealership tech says, "yeah, that happens with some vettes. Don't know what to do about it, sorry." Well a lot of people here know more than most of the techs I've talked with lately. Any ideas? Thanks.
The removable top rattleing is a well documented issue for the '08s and possibly earlier C6s. A TSB exists for the '08s to replace certain hardware on the lockdown levers. You should check out if the TSB applies to '05s.
The TSB is the second-to-last post on the last page. If the car is out of warranty (and I'm assuming that your 2005 is) GM Parts Warehouse (Gene Culley) has decent prices on the replacement handles. His contact is on the left of the Forum amongst the Vendors. Be sure to do the lube procedure on the TSB, it's a big part of the fix.
Also, since it's a 2005, do a search for "roof delamination" as that may also be a factor. Oops!, just saw that you have the clear top, I don't think that has the delamination problem.