Dish soap can help get the new window felts and moldings squeezed into place, and help get the window glass back into the new rubber parts. Be sure to grease the tracks the window rollers ride in. Be careful with the glass, its not easily obtained!
Before you reassemble anything, check for cracking where the window frame is attached to the doors. I've had to weld up cracks that develop at the front and the back where the window frame attaches to the door on two SX/4 driver side doors. Years of slammin doors with dried out rubber and the weight of the mirror makes cracks form in those locations, but its easy to stop-drill the cracks and weld them solid again while you have the glass and rubber out. The window frame can flex independent of the door when there are cracks in these locations, and the mirror rattles when the door is closed and vibrates while driving. With any cracks welded up, the mirror won't vibrate as much or seem loose on the body panel any more, and the door will close with more of a solid sound rather than with a rattle. When welding, mask off paint, interior, and keep all glass away from sparks. I had to repaint some of the exterior body panel where the cracks had grown onto the outside, so I had to weld some of the door skin where the cracks had grown. The welds were a series of small tack welds to stitch up the cracks, which I then ground flush with the door skin, then did the touch-up painting with the closest match I could find in Dupli-Color.