picked up 05 GT vert, minor issues

So I picked up an 05 GT vert this weekend with 39k miles. Ford included their platinum care 4/100k warranty as well. Not really all that consered because most things will be replaced with upgrades anyway.

Only issues I notices was the rust bubble under the good that I know is a common issue and I'm not too concered about it, brakes are slight warped so I'll be ordering some, and the rear quarter window on the drivers side doesn't go all the way up. Its literally stops about 1/8" from the top. Doesn't feel/look like its binding and the window is tight when I wiggle it. Any suggestions on what to check when I pull the rear interor out to look?

Other then that, I'm really happy with the car and I am planning on long tubes, catted x-pipe- and axle bak, 4.10s, shifter, and a tune.
 
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Found a TSB for the rear window. Ordering the replacement this week and will adjust it properly.

Really appreciating the car more and more. I was a Mustang hater by association for too long that I was practicly brain washed.