I loosened the caps and used a pry bar (hammer did not help) to wedge it front and back. No more than I had before. I guess I got to pull the crank back out and make sure there is nothing amiss.

i think i'd buy another bearing set, as much as that would suck to pull the crank and start over. you sure you don't have a cap reversed or anything else worng? you're only .001 off, but might well be a mile.

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ICON Motorsports

1st & 3rd
MM Black Diamond 538 F&AM

I think I will take it back out and put some blue layout dye on it to see where it's touching. Maybe the radius on the crank is more than the bearing.

I pulled it back out and the radius on the bearing and crank look good. With the bottom half (top actually) still in you can tell that only about the middle inch of the bearing is actually touching on the crank. Not only is the some space in the radius, but the bearing has a little space that it drops down before starting the 90 radius.
I took both bearing halfs and slowly sanded them with 600grit on a pane of glass. I thought that I had actually taken off a little (used two sheets of 600 up). and when i put it back, i got about .004 with the crank sitting on the top saddle. When I put the rear cap on and torque it down, it drops back to a little over .001.
Its going with a manual trans, I think I will be able to open the trust up after I press the clutch a few times.. but I hate to burn it up before then.