And here is an update:

Just now for the heck of it, I pulled the #3 cap off, hammered the snout with a dead blow hammer so the crank is all the way back, slid the cap on and very very carefully made it go down into the seat evenly and pushed the cap as far forward as possible (my thinking was this lines up the bearing in the cap with the bearing in the block). Then I tightened the stud nuts in 5 pound increments starting at 20 ft*lb working my way up to 100 ft*lb, spinning the crank at each interval to check the tight spot. When it got to about 30 ft*lb I could start noticing the tight spot... then I actually made it all the way to 100 ft*lb and can still spin the crank with one hand... but the tight spot is still there... however I can spin the crank 360 degrees with one (strong) hand now.

I will try reaming the hole with a 17/32" reamer like Johnahah said first and see what that does. 17/32 actually would give me 0.531" which seems like a big change from my current 0.503"... maybe they make a 33/64" (0.515") reamer?? Or should I just go to 17/32"?

I'd deal w the stud OD to cap hole ID 1st (find a bolt to mike it) & I think when you duplicate the oe bolt to cap clearance that you'll be set and the end play will be OK since you had 4 thou w (1) bearing half in place which is fine and I got a feeling when the above is resolved & the lower bearing/cap installed that your end play will be the same (or maybe .0005" less) which is still perfect.

360 main cap oe bolts. went & checked: 1/2". the threads and the shoulder under the head are both 1/2" and the shank between the threads and the shoulder is 7/16" (checked w cheap plastic calipers, all I had when I was over there).