It's most likely either the clutch hydraulics, or the linkage up to the master cylinder pushrod. One common culprit is where the "knob" on the linkage off the pedal goes through the eye-hole on the pushrod. There's a craptastic plastic bushing there that, when it wears, the pedal doesn't push the pushrod far enough. Two effects of this: (1) doesn't close the starter lockout switch, so it's hard to start, and (2) doesn't fully open the clutch, so it's hard to shift (grinds). Sounds exactly like your troubles.
Two fixes - one involves cutting off that eye and replacing it with a Heim joint, available on eBay. The other is less elegant, but simpler. Cut the four "ears" off that crappo plastic bushing, put it back on, and on the part of that "knob" that protrudes through the eye-hole, you put on a drill stop collar (the kind you put on drill bits), 7/16", and tighten it down. You can also completely replace the plastic bushing with a little piece of brass tubing, 1/2" OD x 7/16" ID, cut to fit in the eye-hole. I've done this on both our trucks; both are working perfectly going on two years.
It might also be the master/slave themselves, but with the starting issue, it's more likely the above.