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I have a 97, originally with a plastic window, that I've put a 03 glass window top on, and I have exactly the same problem. Mine will 'settle' into place after a bit of driving. I've tried various things but can't get it right, so have pretty much ignored it now.
Some things to check though...
* does the clamshell sit correctly when the top is closed? If it's raised then also, there's 2 plastic 'sockets' on the body under the clamshell that rubber stops on the clamshell fit into, these can be turned to raise or lower where the clamshell sits.
* have you checked the drive cables (that run from the convertible motor under the clamshell to the transmissions on each side) for wear? if these are old they may not drive down the top with enough force at the end of the run.
My only other thought is as Anker says, that the microswitch is saying it's fully 'open' a little too early, but as the switch is built into the newer transmissions I'm not sure if this can be adjusted?
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