Check - disk in the correct orientation. I checked and double-checked this during the install. The disk actually had a sticker on one side which said "This side toward Pressure Plate." Additionally I matched the orientation of the disk I removed.-- Are you sure you put the clutch disk in facing the right way? It is not reversible, there is a pressure plate side and a flywheel side.
Check - all new disk, PP, T/O bearing and input bearing. I ordered them together as a kit.-- Are you sure you used the correct clutch disk and pressure plate combination? The 3-puck disk must go with the 4-finger PP and the 6-puck disk must go with the 3-finger PP. It is my understanding that they are not interchangeable.
Excellent thought - I had some trouble getting the tranny in, it's totally possible it buggered up the input bearing a little and is now binding on it. I will check that and post up. It will probably be this weekend, as I am trying to get a new house ready for move-in. The timing on this is horrendous. Better though than if it would have gone on me during my 750 mile recovery-- I'm not sure I trust your transmission adapter (the aluminum ring the transmission bolts to)..... I'd make sure to check it. There is a procedure in the TM for checking it's concentric-ness. I probably would have replaced it when I saw the thread repair coils. It seems that if you have the correct free travel at the pedal and all the above things are correct, it's gotta be something odd like the transmission's input shaft binding in the clutch disk splines or pilot bushing. The amount of disk material and the wear to the pilot bushing could also indicate this....
Death: I did grease the T/O bearing, and the movement along the input shaft is fine. It's just that when I depress the clutch for some reason the tranny doesn't disengage. My money (for now) is on Johns suggestion of the input shaft binding on the input bushing. I appreciate the post - always helps to have folks remind of all the different steps & parts to ensure nothing gets overlooked.