The MADD wiring information is very helpful. The stock wiring has issues with corrosion and increased resistance at the bulkhead connector, so don't run high amperage through it.
Also, remember that upsizing the grounds from the alternator to the block, chassis and battery to the same size as the positive cables you run allows the charging circuit to flow equally through positive and negative circuits.
I run a rewound CS 144 with a heavy duty bridge rectifier and basically the MADD wiring.
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