I had similar issues a few years back. The issues I had Dealt with were the centerline of all the parts, but also the tilt of the trans from front to back. Once that was resolved I had a slight issue getting the pilot bearing and the shaft on the trans to go together the rest of the way. I ended up putting an extremely light coat of high temp grease on the tip to get it to slide into the bearing.
Taking the two bolts and cutting the heads off to make guide pins for the trans are worth their weight in gold for me. Allows me to focus on alignment rather than lifting and alignment.
Good luck.
Last edited by Yelostn78; 04/17/2013 9:44 PM.