The AMA never disallowed 4 cylinders engines. They relaxed the CC limitation to include 1000cc 4 cylinders. Previously, 750 cc inline 4s (then later upped to 800cc..notably Eric Bostrom riding the ZX7R ) were permitted to compete with 1000cc Vtwins. The TL-R was never meant to compete in the AMA superbike races as Suzuki already had the GSXR750. (ridden by Aaron Yates, Jamie Hacking, and Mat Mladin)
The 900RR is NOT a dud. Honda was never renowned for making race bikes. Not until recently were the CBR lines competitive. Honda made street bikes first, race bikes second. The 900RR was ground breaking as it was the first bike to have 600cc (at the time) weight, with 1000cc (again at the time) power. the 900RR is still a very sought after motorcycle. It's not competitive in the realm of racing, but wasn't ever designed as such. Sure, they were raced, but primary focus was still street bike oriented.
The 900RR was THE bike to own.