Re: Running two 12 volt batteries
Probably because you ran both batteries down and when you fired up the engine, the VR saw 1/2 the resistance is was designed for (with 2 discharged batteries in parallel) and the current it was asked to supply was excessive, causing excessive heat in it and thus causing your problem. Interesting that the batteries had adequate power to start your engine yet provided an excessive load to your VR....may be more to it than appears.
Course this situation is hard on alternators also. I know when you purchase a new battery, at AutoZone at least, they have instructions that you should insure the battery is fully charged prior to connecting into the electrical circuit of your vehicle.
I have a couple of things for you:
1. Some heat sink paste installed between the VR and mounting plate will help the VR to stay cool (Radio Shack has it....called thermal grease...white creamy paste in a tube).
2. Usually, VR's have current and voltage limiters which limit the amount of each under varying circumstances preventing the VR from burning up with excessive current and prevent the Alternator from overcharging batteries with excessive voltage. Possibly your VR was due for a replacement. Still thinking......if your connections at the wiring harness/VR connection were corroded they could have gotten abnormally hot with the extra current and that heat could have easily been conducted into the VR and fried it. If this is/was the case the terminals as well as the adjacent wiring may be burned/discolored as proof...smoking gun.
I have my (1) trolling motor battery and engine battery connected in parallel rather than having 3 total batteries. I assumed I could get away with that, which I have, because I don't run the trolling motor that long before cranking the engine and relocating, and it seems to work just fine.
HTH,
Mark