Misaligned Windows?

Hi all, I just got a 98 mustang convertible gt from my folks in need of some minor repairs. I already have odometer cluster gears and a new windshield cowl trim ordered and working on getting rid of the paint transfer/scratches...

The problem I'm looking at right now is the front passanger windows and the rear quarter windows don't seem to be matching up, either like the front windows are pushed out wards too far or the rear quarter windss are pushed too far inwards. There is a noticeable gap where they should meet, and I'm afraid it might let water in. Any ideas on how to go about troubleshooting/fixing this?

Also, the driver side front window seems to be leaking around the seal at the top which is connected to the top. I'm Guessing this is from the seal being deteriorated and just needing to be replaced.

Thanks for any help!
-Noobie

I figured I would reply with what I found what was wrong, in case anyone has this same problem in the future... The seals/weatherstrip on the roof have stiffened to the point where they don't "give" and block the window from assuming its correct position when closing the door. If I lower the window then raise it back up, the window will seat correctly. When shutting the door from outside I can manually ease the window into the correct position. I'm pretty sure this same issue is causing the leak, and I'm assuming the correction will be replacing the seal/weatherstrip component.

creek, thanks for the response as well As for the cowl trim, it's shattered and cracked pretty badly, hence the replacement part ordered.