FITTING KNUCK ROCKER BOXES ??????

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

Make sure that you have all the end play out of the rocker shafts before you tighten down the 3 vertical rocker box bolts. If any of the parts are strangers to each other, do not even have the 3 verical rocker box bolts in the holes because on more than one occasion, I've seen where I had to open up one or more of the holes because of misalignment.

Failure to do any of this may result in broken ears on the heads or the box.