Robert;
It's easy and valid to say that NOTHING is "fail proof" or perfectly safe! (as I recall, one of the guys that walked on the moon died when he slipped in his bath tub)
Although I can see nothing technically unsafe on running the wire through the cabin, there is OBVIOUSLY something on your mind. Thus, ease your mind and run it outside, on the frame rail that doesn't have the fuel lines.
There are a couple things that seem strange to me in your explaination of what you are planing on doing. For me, it's ALWAYS been best to keep it simple and follow paths that have already been done. Here is what I'd recommend;
Use a vented battery box and make sure that the vent exits the car. Make sure that the battery has a solid hold-down.
Get an SCCA battery shut off switch that can be turned off from outside the car. The reason and thinking on this is so that the fire people can turn off the battery if there is an electrical fire. Mount the plunger OFF button under the bumper where everybody isn't messing with it, but you can still get to it should a problem come up. (personally, I'd have the switch so that it can be only turned off AFTER opening the trunk)
Run the hot line from the battery to the switch, and then under the car to a Ford solenoid mounted in the engine compartment. From the same terminal on the solenoid, run a large gauge wire to the alternator with a fusable link nearest the solenoid. (this is assuming an internal regulator alternator)
Here are a couple other things to think about (that others may contest);
Unless it's a "latching" relay, you should never use a relay in a constant "on" state.
EVERY connection is a possible point of heat and problems! Keep them to a minimum!
EVERY item added in the electrical string uses some amount of electricity and will generate heat. When working correct it should be a very small amount, but it still exists.
If you feel the need for the 100A fuses, carry extras. Or you could try locating a resetable circuit breaker (try boat supply places). Also keep in mind that there are fuses that pop fast or slow. In other words, a 100A fuse that is designed to pop slow would allow "spikes" over the rated 100 amps.
Always use grommets! Always use Adel clamps on the main wire that have rubber jackets (aircraft supply shop) to prevent any movement of the wire.
Sorry about being so long winded!!!!!
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Wes. Vann
Technical Reference & Wagons sections
Gold Member #5