I just put in a GM crate engine. It started up and ran fine. It sat for two days and the battery is now dead. I jumped the car off and the reading at the alt. is 13.5V. It was reading about 14.5V before the battery went dead. Is it reading that low because of the dead battery or do I need to look somewhere else for a problem?

Charge the battery with a charger, not the alternator, and check it again.

13.5V is too low, it should be charging full with a low battery.
68 Chevelle I assume?
What type of regulator?

external regulator