I know it's been a long time since you posted this question, and I hope you've resolved your window issues.
For those that have the same problem, my experience with Panther Platform cars 1992 on has been the window regulators are the cause of that particular problem.
This is usually indicated by a working window switch- the motor turns, but the window won't roll down or up (or comes partially down and hangs, then won't come back up without "manual assistance").
They used a nylon coated steel cable on the regulators, and the coating would harden and flake off, exposing the steel filaments of the cable. Gradually, the filaments would break and the cable would fray and then become tangled on itself inside the cable reel of the window regulator.
Ford's solution is to replace the regulator. Supposedly this problem was limited to 1992-2000 Panthers, but I can't confirm that, as I just picked up a 2003 Grand Marquis three days ago (interestingly enough, Front Passenger window won't work, but that appears to be a bad motor).
We have a 1997 Grand Marquis GS that has been plagued with this problem, as well as bad switches. I replaced the original Driver Door window regulator with a cheapie from eBay, which lasted about 8 months. We had a Ford dealership in Dothan, AL replace it in 2009, and it failed last last year. While they claim to have eliminated this problem in 2001 and later models, the replacement regulators don't seem to be a long-term solution, either.