Thanks for all the replies.
To answer some questions; Guy- the block was not align honed. The machine shop called me after they inspected the motor & told me that the engine was in good condition & it wasn't required, if I wanted them to do it, they would, but suggested I save the money for something else. When I assembled the motor, I double checked everything with plastigage & it was all spot on.
I also had the same thought as to the oil pan with a built in windage tray, however I wasn't able to find one for this motor.
I have to agree with all of you. I can't see it making any difference at all, but I'm no expert so thats why I wanted other people's opinion. The main caps are exactly like Bogie describes, they sit into a relief in the block, the bolts don't have anything to do with the alignment of the cap. Bogie is also correct in that the caps are all marked 1 thru 5 with an arrow pointing to the front of the motor.
I feel a lot better about this now.
Thanks again to everyone who took the time to respond, I really appreciate it!