I ended up calling American Diesel to order some other parts and asked about it. The contact on the injector pump is for cold start. It's wired to the switch in the header tank. Brian said I should simply disconnect it, because the only time it will kick in is if the engine is ever started below freezing - since this will never happen, it is unnecessary.
The black thing with the wires coming out of it is a relay for the stop solenoid. My stop solenoid has been on the fritz, he said these things cause lots of problems, and to simply replace it with a cole hersee like you see on the starter.