where to start looking for a battery drain problem.

I have a 02 F-250 with a 7.3L Powerstroke. I changed it from the after market flatbed, to the normal short box they come with on Friday night, and Saturday morning the batteries were completely dead. I couldn't even get my doors unlocked with my remote. one battery tested at 4.0 the other at 5.4, dead enough that the part store couldn't even tell me if the batteries were bad. I charged the batteries and had them tested again, and they tested fine. I then bought a new alternator and put that thinking that was the problem. I drove to a friends house were I let it sit for 4 hours. it was as dead as it was that morning. We jump started it I drove it home and turned it off and tried to start it again, it was instantly dead, I lost all power. I'm going to check the grounds to the batteries, and the wires in the box...... What could be draining two batteries that fast though? Thank you for your time!