I have an la 360 I'm building and I noticed the first main bearing halves don't line up on one side. I took the cap off and made sure that half of the bearing was seated properly and it didn't make a difference. Could it be something with the cap still or do I have to take the crank back out after I have basically the whole shortblock done with now?

 

As long as all the caps are back on the sattels in the same order? you should be good to go.
But if you got the wrong crank radius or the wrong bearings or the caps mixed up.
Then yep.. Your going to have a issue, and apart it come.

 

I think you are trying to make something out of nothing it's just the way it is made...