On the alternator there are 2 types of gm internally regulated alternators one has 3 wires like our original externally regulated alternators but uses a flat plastic plug instead of a square one like our originals and the other type which is more modern then the former uses just one charge wire from the back of the alternator to the battery and is self energizing. It sounds like you are using the latter true one wire. The other 2 smaller wires in the plastic plug you are talking about were used in the original setup and in the 3 wire internally regulated alternators. One to the key switch to energize the alternator and one to the charge indicator lamp in the dash. Obviously you don't need the one that is switched by the key to energize the alternator in your one wire self energizing alternator so you can cap that or use it for keyed power for something else if you want. the other wire for the dash light can be capped but you will have no gen/alt. light. If you are using an aftermarket volt gauge then you don't need it anyways. I don't like 1 wires because I like to run original stuff But if changing to an internally regulated alternator I run the 3 wire for compatibility with the factory wiring, you just have to change the one different style plug. As far as the starter not disengaging That sounds different from what Bronzebird is describing in his post about a running engine that can't be switched off. If the starter solenoid is only engaged and engine turning over in the start position and with engine not running but key in the on or run position does not turn over. But after the starter is engaged with the key in the start position and the engine starts but the starter gear wont disengage with the flex plate/flywheel that is a mechanical problem. Only 2 possible problems cause this the first is a starter gear that does not have the proper clearance from the flywheel and needs to be shimmed to the proper spec. I think the spec is one sixteenth of an inch but don't go by my memory. You can use a drill bit between the 2 gears to get your measurement. There must be videos on YouTube describing how to do this just type in how to shim a gm starter It is a very simple procedure and should be done whenever installing a new or different starter in your engine. You could get lucky and it be dead nuts right out of the box but in my experience as a former mechanic most people don't have an experienced enough ear to be ale to tell if the gear depth spec is to big or to little as long as it works and does not sound terrible. The problem is down the road in time when the flex plate/ flywheel teeth corners get all chewed off and by then it's to late. If your gear depth is in spec then the starter has a mechanical solenoid problem which in most cases will show up in a simple bench test.