2003 Astro quit and troubleshooting found an orange spark. So I replaced plugs, wires, coil, and distributor. All one at a time to ensure no mixup. But when I tried to install new distributor it wouldn't seat correctly. I did mark the rotor position. I found only one spot where it would seat so buttoned it down and tested. No go. I tied original position and it finally did seat but still wouldn't start. So I decided to step through all possible rotor positions, testing each one, clearly marking rotor position and jogging the engine back to where it was before the test. The fifth test it ran, but rough. Next cog, almost exactly opposite where it ran previously, it idled but backfired. I double checked wires and found 4 or 5 of 6 incorrectly located. I fixed that and the vehicle popped into a smooth happy idle. Runs great now.
It had been running like that for maybe ten years! I hired a mechanic 5 years ago to tuneup and he missed it.
I can imagine that a rotor incorrectly indexed (180°) could possibibly be accommodated by moving wires around for correct firing order, but it seems really weird.
13 teeth on the helical gear divided by 6 cylinders tells me a poor alignment with rotor and cap conductors will result. Only one position will work well. Does that make any sense?