I just completed a flywheel and clutch install. All went well except for getting the transmission to fit back into the bellhousing; the trans input shaft wouldn't go into the new pilot bushing. After three failed attempts at disassembly/reassembly I inlisted help.
Here is the trick:
Install clutch pressure plate as usual, using the allignment tool. Install the bellhousing but only put two easy to reach bolts in for now. Put the transmission in. If it all goes in then just continue with the install. If it doesn't, then get it in as far as possible, mine went all but about 9/16". Then remove the bellhousing bolts and replace with longer ones so that the bellhouseing can be pulled back to the transmission. With the transmission being supported in the front by to clutch plate, pull the bellhousing back to the transmission and install the four trans to bellhousing bolts being carefull not to pull the trans out of the clutch disk. Now you can wiggle the trans/bellhousing as a unit enough to get the input shaft into the pilot bushing. You may need to engage the clutch to get everything lined up.
I wrote this really for the archives. I had a very flustrating time with this step untill I was shown how. Hope this helps someone in the future.

 

I found that I needed someone in the car working the clutch while 2 of use laid under the car and wiggled the transmission.

 

I had to do the same thing... keep the bell housing loose by installing all bolts but keeping about 1/2 bolt length out - bolt in the tranny - tighten up the bell housing. Nice and snug fit.