Super bummed. New motor. Bad bearings?

I'll probably not be taking it back to the machine shop unless I find something wrong clearance wise that can't be remedied with some oversized bearings. That said you can bet your *** I'll be washing the block very thoroughly. I have the engine brushes already. It's not rocket science, but obviously requires persistence.

Any suggestions on cleaning out the rocker shafts?

You have to knock the soft plugs out to clean them correctly.