Anyone use a battery isolator on a dual battery drag car

Can you share some more info about your setup. Do you use an alternator to charge both batteries, and what gauge wire from the alternator to the trunk.
The generator you speak of, are you using the dc output from the generator to directly power the water pump and fan.
Are you familiar with the relay type of isolator that has no diodes?

Duane, Yes the cars alternator charges both batteries. The batteries are wired in parallel all the time. The charge wire from the alternator to the starter terminal is 4 gauge stranded copper. The output of the alternator is rated at 80A. The batteries are connected to the starter terminal with 1/0 gauge stranded copper cable.

No, the generator I have does not have a DC output. It powers an Elgar 120V AC to DC convertor. The output of the Elgar convertor gets connected to the cooling plug.

The solenoid type isolation has it's own issues, some of which are mentioned above. I prefer to never isolate the batteries from each other.
Another way to solve your problem is to simply use a battery charger that will keep the batteries charged while the cars pump and fans are running. Just make sure it's a self regulating charger that decreases it's output when the current load is removed, or you'll overcharge your batteries.