I'll just add my $0.02 here regarding the BFH technique: DON'T DO IT!
To put all this back together and do a proper alignment, you'll be trying to align the coupling faces within .001" across the face. Do you really want to run the risk of banging on that flange with a hammer if you need to realign it later? Not to mention the danger of bending the prop shaft.
Use a puller or hire a professional.
I agree with Arthur, it could be that the stuffing is keeping the threads from grabbing. How many rows of stuffing did you put in? Maybe consider doing it one row at a time, compressing it with the nut, then add another row.
I'd bet money that is the issue and not the threads.