Here's a few things to check...
Make sure that your motor is still tilted to the rear. When you take the tranny off, it will drop a little bit.
Make sure that the clutch is aligned correctly. If it's not, then you won't get it in.
Now this part will sound crazy... while holding it up mostly from the back, pick up the front just a little bit and trun the tranny from the drive shaft end while it is in a gear. What this is suppose to do is align the input shaft with the gear that is in the middle of the clutch.
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