I know this might be a stretch but what are the odds of the seal journal on the crank not being in line with the rest of the crank? or the other way. the crank seal retaining area not in line with the line bore? i wouls at least try to check that part on the crank, seeing that that might be the 1 thing that has changed in the previous setup.
I would think this would show up when I lay crank in mains and set dial indicator on seal journal and it displays .0009" out of round. I called Eagle today and they say they keep it at .0005" or 5 tenths. They were of no help of course.
Also when I have had the crank out and installed the retainers-the seal halves line up nicely and I mean round and inline with each other. J.Rob