Atomarc, Pertronix DOES make an HEI rebuild kit, with a 50,000 volt coil, an ignition module, cap, and a rotor. I bought the Pertronix kit for two reasons. The first is that I used Pertronix electronic ignition conversion kits for breaker-type distributors many times with happy results and I trusted them. The second is that my truck is red, and the red cap matched my truck (admittedly a weak reason, but still...).
It is an early GM stand-alone HEI distributor. It is just rebuilt using this Pertronix kit. When the Pertronix rotor melted, I went into my storage shed and dug out the original GM rotor that I had for it before rebuilding it, and put that on. That's what I meant by that.
The alternator is a 1986 IROC-Z unit, 120 Amp, with 5 rib belt pulley. I bought it for my IROC that I no longer have, but since I'm planning on reinstalling the IROC's TPI fuel injection system, I wanted to use the IROC's alternator as well, since it will plug into the harness. And yes, I do still have the IROC's HEI distributor, but chose the stand-alone HEI for now since I am currently running a carb.
I will be taking the alternator to the electric shop to rebuild it tomorrow, and I will also ask them this question and see what they say about the connections. If I run the BATT wire to the starter instead of the alternator, but the alternator ALSO has a wire to the battery via the starter, then electrically it's all the same I would think. Still, I'm going to make sure before I fry another alternator. I'll post here what they tell me.