Few Questions '02 Vulcan

I recently purchased a '02 Taurus SE, now 48000 mi, vulcan 3.0. First, why do the front windows (esp drivers side) sometimes sound like the track is being destroyed on the way down? Next, the other night I was light throttle up a hill, and heard a scary sort of fluttering/grinding sound from the front (almost like the starter started to engage), let off and got back on gas and it was gone. Also, after a cold start, when in gear and stopped it sometimes seems like, not even a misfire, but incomplete combustion in one cylinder (just barely running rough). And other than that, anything I should keep an eye out for? Thanks.

Am not sure what you hear when you refer to the window noise but Taurus windows have a reputation of making kind of a groaning noise when seating into the top mounting.
When my '02 Vulcan (by the way, both engines are 3.0's) passed 50,000 miles, chirping noises started coming from the engine. Was the driver unit for the cam positioning sensor, most commonly referred to as CPS. Is a DIY project if you have some mechanic experience.

I believe the window problem is cuased by wet or damp window tracks - not sure if there is a way to clean them or not.

Cold start, the car is running richer than when it is fully warmed up. It's possible that letting it warm up another 2 or3 minutes would solve the misfire problem.