Hi,
If you have #4 wire going all the way to the trailer, then a 100 amp fuse is the max size that should be used. You will not get more than 50 amps to travel between the two 12 volt batteries. You will need a very oversized connector, like a forklift battery connector to get more than a few amps from the truck to the trailer. Look for a 50 amp rated 'anderson connector'. It will handle 75 amps without getting warm, and is rated at 50 amps when plugging in and out all the time without a problem.
The wires going through the factory wiring harness are probably #12 wire - rated around 20 amps, and with that distance, probably will never see more than about 10 amps going into the trailer battery.
By connecting a wire directly to the alternator, you will get a full 14.2 volts, while the battery probably only has about 13.5 volts.
Good luck,
Fred.
