Didn't you say you had coolant in the oil? I wouldn't be surprised to see some rusty spots in some places.
Your bearing clearances, if you measured correctly, are perfectly fine for a BBC rod journal. I usually try to set them at .0022-.0025" in a street application. An extra .0002" will not hurt anything.
Did you make sure to put the "U" bearing in the rod and the "L" bearing in the cap? Any evidence of detonation anywhere? To me, it looks like not enough clearance, but just checking other things.
To get a stubborn cap off, put one bolt/stud in the hole in the cap, with a good bit of it sticking out the top, and smack the bolt/stud sideways with a dead blow.