ARP main stud and oil pump clearance

Excuse the runon paragraph, my laptop is broke so I'm using my PS3 and it wont allow me to shift... I have two more question that are relevant. After an align hone, do you need undersized bearings, or a shorter chain? Also, wouldn't the machine shop leave the studs and caps installed? I picked up the block empty. How can I tell if they did a quality job? After all their name IS quality engine, but you can never be too sure. This is my first motor so any help is greatly appreciated.