Thinking about it virtually...It might help to look at the gap all the way around the engine trans. interface then shift, raise, lower with the trans jack to get the gap equal all the way around....very carefully, slowly, minutely. Back it off before doing this. Then try to go forward with it.
Hopefully there is nothing hanging things up on top...perhaps you can climb up top and get some eyes on it
Best of luck....breathe!
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