I stopped by to help a friend install a T5 transmission in his truck. He already had the new pilot bushing installed in the end of the crankshaft. When we tried to install the transmission, we encountered the same problem you had. We could not get it to move the last 1/8”.
The problem was he did not have his pilot bushing installed in the end of the crankshaft far enough. So the T5 input shaft was bottoming out on pilot bushing. He did not apply any grease to the OD of the pilot pushing at the time of installation and it stopped moving when it got tight. We could not get it to budge in or out and had to remove it with a chisel. Another pilot bushing was installed properly and everything was good.
