Yeah, those 1990s era Treks can feel stretched out. The saddle to handlebar drop isn't as extreme as current racing bikes, but they were more stretched out.
My approach for fitting my early '90s 5900 is physical therapy to improve my strength and flexibility. If that doesn't work in the long run, I'll try:
- Raising the bar a bit (spacers or upward angled stem).
- Shorter stem.
- Different handlebar -- short reach, short drop compact bar. Take a look at the Specialized Ruby for an example.
- Shorter hoods for brifters. Or old school aero brake-only hoods, with downtube or bar end shifters.
Keep in mind all of the above will affect handling. The bike may feel twitchy on curves and fast descents.
Also:
- Better bar tape. Most comfortable bar wrap I've tried so far is Arundel Synth Gecko. It's 100% silicone, very soft and grippy, reusable (no adhesive on back, it sticks to itself naturally), and comfortable on rough pavement. It really tames the chipseal and rough pavement.
- Better saddle or shorts. Przewalski shorts and bibs with their orange 3D padding is very comfortable.
Wider tires may not be an option. Even 700x25 is pushing it on my 5900. The later Treks may have room for 700x25, but 28s weren't commonly used back then.
Better tires in 700x23 can help. There are tires more suited to touring or cobbles (Specialized Roubaix or similar) that should be more comfortable. Probably more expensive too.
If all else fails, albatross or North Roads bars, and Selle Anatomica saddle. Ultimate lightweight hybrid.