| I've been trying to get the manual transmission back in and took a lot of pointers from this site. Just wanted to put this out there because I couldn't find any posts on this particular issue as I was working through it. I was having an issue where everything was aligned, but the input shaft did not want to push into the pilot bushing. This was leaving an inch gap between the back of the engine and the bell housing. Try as I might; wiggle, hoisting, tilting engine, etc - I could not get it fully mounted. I got the transmission aligned by using the headless bolt method to create a couple of rails to slide the transmission on and orient it. I still could not get it to mount that last inch.
Things I checked -
- make sure inner diameter of pilot bushing is correct (I don't have dimensions handy) If your clutch alignment tool slides in/out fairly easily after mounting the pilot bushing to the engine, you should be fine on measurement. Mine was a snug fit, but not too snug.
- make sure input shaft spindle is lightly greased with moly
- check that the transmission housing is not rubbing in the tunnel. The top of my bell housing was barely rubbing the coolant line that feeds the heater core. I had to push that hard line up slightly. After ensuring the above, still no dice for me. I ended up drawing in the transmission to the engine with long bolts and washers, working my way a few turns at a time on 4 bolts at different points on the circumference, pulling in evenly. Hand thread the bolts to avoid cross threading. If as you tighten the bolts it is not threading on easily, STOP. It is likely one of the above items is not correct. If you continue threading with more than say 10-15 lbs of force, you likely have an issue different than mine and you can break the bolt ears off the transmission or damage the input shaft. The fit to the pilot bearing should be snug, but you should not have to force it. Too tight a fit can cause issues with clutch engagement/disengagement. Obviously, I'm not a mechanic, but hopefully I have not introduced misinformation. I think most would consider drawing in with the bolts a last resort but it worked for me.
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