My money is on the pilot stuck on the input or the splines ahead of the clutch disc are rusted/messed up/twisted. You mention you can spin the output shaft but ....is the tranny in neutral? If you can spin the output and see the input spin than obviously thats not it. I would try unbolting the pressureplate and see if the tranny and clutch will come off in one peice..
Well on second thought it looks like your seperating the tranny from thge bell which means you cant unbolt the clutch. What was the reason your taking the tranny out?

 

If the wires are all unplugged, and the shifter is out, and your transmission rotates freely, and you have your slave sylinder removed, it's got to be hung up on the splines or the clutch fork. There isnt anything else.

Tilt the whole engine downwards until you have the rear of the oil pressure sending unit close to the firewall, then put the trans jack under the transmission to lift it up slightly. Perhaps that'll pop the splines out of the clutch pack. Maybe you jostled the clutch fork and shifted the clutch off-center and bound the splines up against the pilot bearing. If you cannot pop it loose, put the trans back onto the bellhousing, reinstall the clutch fork, and use it to acutate the clutch once. If the clutch is offcenter inside the pressure plate assembly, it shoudl pop back into alignment and free up the splines. Then remove the transmission.

That's my guess.