I had a !995 Chinook on the Ford E-350 van chassis. It had a problem like yours. Turned out that the 'Isolation(Smart) relay that was supposed to determine if/when to parallel the engine & chassis batteries for charging while driving was bad. Oh....one more interesting thing to kno about that van chassis. There is also an ignition relay thats supposed to parellel the engine & chassis battery. The chassis battery, under the hood on the passenger side runs the TAIL & RUNNiNG LIGHTS!!! If this relay goes bad the chassis batt. can't charge off the alternator. Eventually it goes dead...No tail or running lights but still have brake lights. This relay is impossible to find. Its located inside the bottom main chassis frame where the front bumper bolts on. I relocated it to the area above/behind the radiator.
