I am in the middle of a clutch job on my 99 xj 4.0 ax15. I have gotten the transmission pushed back onto the motor all but the last 3/4 of an inch!! I have tried to wiggle/wobble it on the last bit, but I can not get the two dowel pins to seat into the block. I need HELP!

any tips or tricks to get the last bit together? Can i clamp it in or use the bellhousing bolts to pull it together?

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If the clutch disc is not properly aligned the input shaft won't go into the the pilot bushing/bearing. That's why it's hung up. If you use clamps you'll probably **** something up.

Put a socket on the crank bolt and turn the engine over by hand. Also, stick the trans in gear.

Do not try and squeeze it together with bolts or clamps! It will go in by hand if done right.

Yes I didn't think it would be right to force it together with the bolts. I'm glad I've got y'all to help.

I DID use the included clutch alignment tool and torqued the pressure plate in a cross pattern before I removed the clutch alignment tool.

it should be lined up right??

If you are that far in the input shaft should be lined up and through the splines in the disc. Try tilting the rear of the transmission down just a hair while lifting the front of the transmission up and pushing it forward. Your trying to "hang" the input shaft on the edge of the pilot bearing.
Once you find the right combination and get the input shaft started into the pilot it will slide right on home no clamps needed.

Did you install new pilot bearing ? If so did you make sure it fit shaft b4 installing it ?