I ain't never heerd of an "adjustable" TOB.....that's a new one for me!
On the subject of the flywheel, it's IS possible that machining it over the years has changed the relationship between the flywheel and the TOB some, but I doubt it would be enough to cause your problem. If this were a hydraulic set-up, yeah, I'd be more inclined to go that route, but a mechanical set-up....not so much. IT would have to be 1/4" or more difference for that to come into play, and since you apparently did NOT have this problem before, I can't see them cutting 1/4" off the flywheel this time.
There are shims that go between the flywheel and the crankshaft to re-establish the correct working height of the flywheel, if needed.
I think the bottom line is.....yer gonna hafta pull it out and start over, and double-check everything. 

This particular statement still leads me to think something is NOT assembled properly. A "rumbling" sound when pressing the pedal to the floor means something is hitting something it should not be hitting/rubbing....
It has to be either an issue with the TOB not being installed cerectly, or the disc is backerds....

OK...latest update on this. Pulled tranny out and checked clutch...everything installed correctly. Did a lot of research with different people and there definitely is 2 different length t/o bearings. Took tranny out to shop to have seals replaced and a check out. Immediately upon picking up tranny the guy says something don't feel right when he rotated input shaft. Found bearing under nose cone was coming apart....that may be the rumbling sound. BTW he says I have a Muncie Rock Crusher tranny...a very good tranny...getting rare to find! He also gave me number for the t/o bearings.....for everybodies info the number for the 1.225 inch short bearing is 614018...the number for the longer 1.885 inch bearing is 614037. So I'll have the bearing tomorrow and the tranny may be done by the end of the week....a little late for anything more this year but at least hopefully I have the clutch problem solved. Also did order a new fork and pivot stud for it and the new pivot stud is about a quarter of an inch longer than what was in the bellhousing....that should also move the t/o closer to the pressure plate.

So there WAS something wrong with the tranny! That's why sometimes you have to bite the bullet and take it some where reliable. I'll be keeping my fingers crossed that it all turns out ok! Gotta be ready for NEXT YEAR! Really enjoyed you and Kathy's company yesterday (even if we didn't see much of the ladies).