bmwm750,
I've had two GAHH glass-window tops on my 2000. Although I've had issues with the tops (early window separation issue and installation problems) neither has made contact with the windstop. I never close the latch before fully lowering the top. I agree with Boxtaboy, either it just needs to be adjusted or something is broken causing this problem. I also haven't experienced the rattling issues with either top. Maybe both of the problems are related and point to some type of installation error or a broken part.
I agree engine access is horrendous compared to the OE setup. However, I've been able to do all needed maintenance thus far (air filter, air/oil separator, MAF) without cursing too much.
Best of luck getting it sorted!
ddb
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