I have put a new clutch and flywheel in. I used a clutch alignment tool up until the point where I jacked the transmission up and got it onto the bolts. However it is not going in completely. Is the transmission shaft out of alignment? I actually got one bolt to thread and I can continue to tighten it down but I wanted to make sure that I am doing the right thing. What if I force the shaft in and the teeth are a little out of align?

should I just tighten it down and hope for the best?

This is really common. Rotate the engine (or the trans shaft) a little bit and try again. You need to get the clutch and the tranny mainshaft splines lined up. It will go easy when it goes. Also try bumping the trans up or down a bit, you may have the stud threads hanging up on the holes. I put my T4 motor in the 912 using a winch from the ceiling joists so I can wiggle it around and get it lined up just so without having to worry about dropping it off a jack onto,uh, me.

It takes a little finess but it's not that bad a job getting it lined up. Be patient. No forcing!

cheers
Adam
'66 912, 2.2L T4 power!

Put the trans in gear, grab the stub axles, and turn them back and forth, both in the SAME direction. Helps to have the trans supported at the center of gravity, and to have someone to wiggle it up, down, and sideways. Eventually, it should pop right into place. If the balance on the jack is off, undue pressure is put on the shaft and the studs, making it difficult to fully engage. The Cap'n

Put the trans into any gear with your hand. Have a helper push the trans in with LIGHT pressure while you hold one output flange in place and turn the other a bit. This will turn the input shaft and hopefully line up the splines. A very small amount of bearing grease on the tip of the input shaft can help too.

Cap'n beat me to it.

Good I was right you guys. I thought it should go in much easier than that.