When you install the trans back in leave the top off, disable the ignition and crank the engine with the clutch pushed in. The input shaft should not be turning. If it is the clutch is not releasing all the way or the input shaft is binding in the pilot bearing or hitting the back of the crank. Check it before you waste all that time putting the rest of it back together. You can also put in gear, push the clutch in and turn the output shaft and see if it feels like the clutch is not releasing or something is binding.
I have been burned so many times putting clutches in at work that I learned to make sure they feel right before filling them with gear oil, bolting in the cross member, driveshaft, shifter and floor mat and then finding out something is not right.