pto cast cover doesnt match hole in rearend casting

ok so a while back i had posted about a bearing failure on the pto on my 77...i had replaced the main cast lower unit with another i had because of a bearing groweling and when i put the long shaft back in it, the retainer with 3 bolts didnt want to snug up..thus ruining the bearing when i started it as i pulled it in with the bolts ( i know but was in a hurry) so when i pulled it apart and cleaned everything and installed the long shaft into the lower unit the bearing sticks out just a little bit past the housing..no problem cause the rearend has a hole for this...well when i put just the housing on and got it bolted up it doesnt match up with the hole in the rearend housing..off by about an 1/8 of an inch which is what i think caused the 1st long shaft not to seat as it was supposed to ..so yesterday i didnt tighten the housing until i put the long shaft in and snugged it into place...the casting #'s are both 1570 so what happened here ..there is not enough slop in the bolt holes of the housing to raise it up to perfectly center the unit with the rearend...has anyone else encountered this?...do i need to grind out the rearend housing some more..is there a shim that im missing to keep the bearing on the long shaft from protruding past the housing?...thanks for all replies

The first thing you do is make yourself 2 long 1/2 inch alignment alignment bolts for the gear housing . Hang the gear housing from that and then install the long shaft. By having the gear box hang loose you can center the bearing in the transmission case. Once you have the bearing centered tighten the gear case then remove the alignment bolts and replace with the other 2 bolts and tighten. Clear as mud?

yes sir and thanks for your reply... i will get busy making some alignment pins and try that way..thanks again