I just bought a 1988 F-150 with a 5 speed and the clutch slips due to somthing going wrong with the hydraulic clutch cylinder. It finally grabs right at the end of travel (with your foot off the pedal) could there be air in the system?

No, if there were air in it, it would gab early, not late. Just as it would release right at the floor, if at all.