Mine did the same thing. During a recent rear main/carrier seal replacement to cure a BIG leak, I figured for the price of the parts I might as well get a new clutch installed. Glad I did. The TOB was absolutely shot and the pressure plate was missing a few finger tips. The clutch surface itself was fine - it hadn't been slipping at all. But as mentioned above, shifting was tough, reverse was an occational bitch, and the pedal action as all the way to the floor and HARD. After the clutch job, it the trans shifted like my wife's first CRX Si - smooth, effortless, no more notchiness. Also, for whatever reason the car's ride smoothed out A TON after having the subframe off and reset.
I'd also suggest during a clutch job to change the trans fluid, as you can pour it out completely w/o having to drill any holes in the case.
As an aside, the rear main leak turned out to completely be the carrier seal. It was improperly installed at the factory, missing one of the bolt holes ENTIRELY. I guess after 45K miles that part of the seam had shifted just enough to finally start leaking like a sieve.