Count your blessings that you damaged a shaft and not broke the ear off of the head! It is important to assemble once without the lids and seals to assure that you have proper endplays. I usually then seal up in the manner that has given you fits, but the alternative is secure the boxes first, and then to use a bunch of nails to align the cover's holes and then pry the lids into place. This does not always seal nicely.
Are these early, or '41 and later boxes? The seal arrangements are different....Cotten