I am glad that this thread has reappeared. First of all I would like to say that I know Bret and Janet from elsewhere in the motorcycle community. They are the greatest!
The point that I would like to make is. I just purchased the 94 TW that was loaned to Clarke for them to pattern the mold. I would have thought that the tank would fit perfectly. Surprising it fits like all the others. My 99 fits better than the 94. I have wondered if the pattern bike might have been tweeked in some way that made it different from the rest. Now it appears it must be a manufacturing glitch rather than a bent frame.