1996 Honda Accord Clutch out?

The clutch pedal is soft until about 1/2 way depressed. Can't shift in / out of gear smoothly when at a stop, but can find first, reverse, second sporadically.

Can drive it a bit, so we're hoping it's not the tranny.

It's been sitting for a year (son is off to college). It started in about 5 seconds! I'm going to crawl under it and check the trans. Fluid, but that's as far as my knowledge goes. Did his "speed shifting" destroy the clutch? Are there adjustments to say, the linkage, pedal? I've heard $600 too $900 to repair, which is about what it worth! Help - before we tow it in for a diagnosis.