I assume the engine builder knows how to 'set' the crank thrust by using a mallet to tap the crank forward and back BEFORE tightening the main the thrust is on?
I believe you know what to do:
As Yeti said, make sure the trans isn't an issue.
Since it's coming apart...
It's clear that the thrust was not the ONLY issue, as the rest of the bearings don't look good, either. The main bearings should clue you in to whether they are in alignment or not. If they were out of alignment, the wear will be inconsistent from bearing to bearing... and you should do a line hone to check/correct it. Were the rod bearings trashed as well? If so, it's likely a dirty assembly, or the issue with water in the oil.
Plug the bypass.
CLEAN, CLEAN, CLEAN everything during assembly!
Triple check all clearances.
Set the thrust.
Cross your fingers.
Good Luck!