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Did you download the manuals? They include wiring diagrams. There are a number of places that have diodes for radio noise suppression that can short out. Warthog has posted pictures of these in various and sundry threads.
The simplest way to troubleshoot electrical circuits is break them in...
There it is....... gen2 charges the back battery which is only used for starting. After several starts the back battery is too low to crank the engine.
http://www.steelsoldiers.com/cucv/60698-more-alternator-electrical-questions.html