Do whatever you want with it other than painting it. Just put the original parts on the side. No offence to Treks, but very, very few go for more than $300 on Ebay-pretty much high end walmart prices-.I would,and do, just what I want with relatively inexpensive bikes. There just isn't enough collector interest(or more importantly $$) to inhibit changing it to your liking.
Besides, some changes will increase its value. There probably isn't a Trek in the world that wouldn't increase in value if Campagnolo NR parts were substituted for the OEM parts(granted, it wouldn't be cost effective, but they would be prettier).
Do what you want,and put the old parts on the side.
Luck,
Charlie
PS The same doesn't hold for vintage Brit,Italian, and even French bikes, or the pricy Schwinns.However, the NR probably holds for many of them that came with Japanese components.