I would check the fuses. It is very common to draw too much current with a low battery voltage. I'm not sure I understand the chassis battery would ever be routed through the "battery control center" not that I have heard of that term. There is a systems panel control panel that usually has a battery meter in it. The only time the "chassis" and the "house" batteries are connected is when the engine is started. Another potential issue is depending on how you disconnected the alternator if you didn't tape up the end it could have had a short to ground which would have created additional problems.