If I understand correctly. The cups will have a tendancy to unscrew opposite the direction of crank rotation? If so, they are indeed in "reverse", I didn't relize that Trek had made some like this in the past.
I just stripped everything but the front brake, shortened the chain, went with the 40 tooth crank, repacked the head set bearings (they look brand new), greesed and reinstalled the stem, and took it for a ride.
It seems to ride ok and I do need to tighten the BB up a little, but for right now it's a single speed. Actually it has enough room in the drop outs to do 2 gears by moving back and forward in the drops.
Thank's for the help all, it has been a learning experence to say the least!