Clutch issues. Can't put gear in while engine running

Generally to pull it you:
1. Drain trans and pull drive shaft
2. Disconnect shifter and linkage and revise switch wire
3. Disconnect clutch linkage and speedo cable
4. Support trans and remove trans bolts to bell housing and drop cross member
5. Slowly pull trans out straight out the back of the bell housing, making sure that the weight of the trans does not 'torque' the trans input shaft in the clutch disc. A moderately strong guys can drop or install a trans lying underneath, but especially if you are new to this, a floor jack under the trans is the best with this size of trans. If you can borrow or rent a trans jack, that would be great, but I make do with a standard floor jack and just be careful to keep the trans balanced on it.
6. Remove inspection plate on the lower front of the bell housing, and then unbolt bell housing from engine and remove. The clutch lever and throw-out bearing comes out with it.
7. Remove the bolts holding the pressure plate from the flywheel, and it and the clutch disc will come off
With experience, this is an easy 1-2 hour job. (Me and 1 other guy once changed out a clutch on a rally car in 45 minutes!) Plan on 3 hours or so your first time to remove.

The re-install, it is the general reverse except that:
- You HAVE to accurately center the clutch disc with the crankshaft center just before tightening down the pressure plate bolts. There are clutch alignment tools for this.
- When reinserting the trans input shaft into the clutch and bellhousing, you HAVE to 100% to support the trans and not let the weight 'hang' off of the input shaft in the clutch splines; this will bend the clutch center and ruin the clutch disc.