[pippintook]

I just picked up my block from the machine shop.
This is the second time the block has been in the machine shop. Initially my main bearing clearance was a bit excessive (around .004). See my post '400 assembly: main and rod oil clearance not within spec, what can I do?'.
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I brought the block back into the shop. The main bores were on the high side of spec while the crank main journals were on the low side of spec. The machinist decided to align bore the main saddles. The machinist cut "..a few
thou.." of the main bearing caps. No material was removed from the block. He then did the align bore. He measured the rear main bearing clearances and they were .003.
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I got the block back and I am just test fitting my BOP viton seal right now and posted yesterday
to see if guys thought my seal fit looked ok (see post 'BOP viton seal; Does this seal fit look ok?').
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A few guys have mentioned that I may have a rear main bearing alignment problem. I would like to get some more advice before I ask the machinist about this bearing alignment. I will post a few pics of the bearings.

Questions
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1. So, this alignment is definitely not acceptable and I can not run with the bearings being misaligned?
2. Could the cause of the bearing alignment be an improper align bore/align hone?
3. The alignment of the BOP seal looks ok, should not the seal also be out of alignment if there is a problem with the align bore?
4. How would I fix the bearing misalignment?
5. Any other advice before I go back to the machine shop?