battery getting drained while driving

Jez. You don't need 2 electric fans drawing 48 amps. I had a single 20 amp fan on my Rat motored tool truck hooked up with a relay and temp switch and it barely ran, even in 90+ temps pulling 16,000# load. You may need to rethink your combination. You mentioned you have a trunk mount battery. Is that when the problems started? Don't trust the battery in the trunk to be grounded well there. I would run a separate ground cable to the block and make sure the body is grounded well from there.