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It's not in all the way. It should all be behind the bellhousing so it can reach the motor. You must have pulled it out of the tranny some when removing the motor, the way I get a convertor in when I do them is spin it, and hit it with my hand a few times till it lines up right and goes in. I don't know about any damage that could be done so far as I am no expert in that area.
In the photo's you can see the snout of the tc has the paint removed
from it where it bound to the crank.
Both sides of the tc have to be checked along with the pump.
(tc is a cheap stamped steel type)
Also pull the input shaft and check for bend.