Same thing happened to me, after a spirited run down the interstate in my '97 integra, it started having problems getting into gear. It would only shift at around 1200 rpm if at all.
After replacing the master and slave cylinders (to no avail, but they were bad worn anyway) I pulled the transmission out. To my surprise, I found that the Clutch disk had malfunctioned and puked up two of its four springs. They had broken out of the keepers in the clutch disk and were rubbing against the flywheel and causing all kinds of hell. Scratched up my flywheel pretty bad.
But... it machined out clean, and gave me the chance to install an exedy stage 1 : ) I couldn't be happier. New hydrolics, new clutch, pressure plate, throw out bearing, fresh flywheel, Gawd, that thing shifts buttery smooth now : )
that was a hell of a long story. Check your clutch cable, clutch adjustment/freeplay. If its all in spec, its time to yank the 'ol tranny and put in some go-fast parts : )
Good luck!