We had persistent leaky windows on our Amtran too. Amtran is apparently known for leaking windows. We pulled all of our windows, cleaned the metal window assembly with acetone and a wire brush (using a drill attachment) so they were spick and span clean. Those suckers looked brand new! Then we cleaned the mating surfaces on the bus itself, down to fresh paint (removed any traces of butyl tape). Then we use 3M Dynatron 550 on all mating surfaces and put them back together. This was a solid 2 days worth of work. It wasn't all that bad, truthfully. Put on some good tunes and have a partner to help ya. Having said all this.....the windows STILL leaked. Especially in the corners.
It turned out that the water was coming in at the bottom of the glass, where the rubber gasket is supposed to seal the glass-metal union. The rubber was a bit dry rotted and it let water into the metal window frame, where it travels down to the corner and to the inside of the bus. Our temporary solution was to put a strip of clear weathersealing tape at the bottom of the glass, covering that gasket. It works like a charm. Our plan is to just caulk over that gasket, but we've got many other projects ahead of that.
Bottom line? Try sealing the rubber gasket before you pull any windows....that just may be the ticket and save you lots of frustration.