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Sorry for letting this thread get sidetracked. Lets keep it simple for now and learn all the hard stuff later.
You current wiring works, you might need some new cables and terminal ends. Fix what you have and then get into all the theory about isolated ground alternators, dual batteries ...
The factory wiring terminals have been replaced. They did rewire it the same a stock.
1) The yellow wire is a ground. The factory wire was black and was attached to the radiator support. It was 10 gauge.
2) The smaller red wire on the rear battery feeds the diamond shaped 12v Positive terminal...
The wire sizes are listed in the wiring diagrams. You need to read the first few pages of the Troubleshooting section to see how the wires are labeled and what the numbers mean.