I apologize I don't have any direct experience with the add-on alternator, so just take this with a grain of salt, but it appears looking at the wiring diagram that you want to splice the brown wire(s) into your ignition signal. If the terminations are a male and a female bullet plug both connected together, then I'm sure this is right, just hook up the male one *only* - it has an unused female mate somewhere along the chassis hanging out of a harness nearby, which is also a brown wire.
I am looking to add a belt-driven air compressor to my project and am interested to see pictures of how your alternator kit mounts, once it's in there ...