Pertronix, Timing, overheating & lesson learned

I have a 1965 Buick V6 225 in my 58 jeep, over heating at higher RPMs ie speeds over 50 mph { No RPM gage& no overdrive} & Double check timing with light good every time 5* BTDC with vac off & plugged, get a loud back fire out exhaust every time motor is shut down.
After beating my head on a wall over this I decide to get back to the basic and start over.
Leaving distributor in place I removed Pertronix system and reinstall points & cond.
Set the dewell at 30* put cap on and recheck timing.
!! No timing mark showing up with light. Now I’m thanking what the heck is going on! it was there with the Pertronix system and I did not move the distributor. so I pulled the #1 plug and bring motor up to compression stroke TDC. pulled the cap off distributor and there it was - One Tooth off !! between number 1 & 6 cap plug towers.{ I had pulled the distributor to install the Pertronix and put it back one tooth off and did not double check myself} Lesson learned here.
Corrected my screw up and fired her off, set timing, much better, no overheating, no backfiring.
Now just wondering-
1. Why was the timing mark looking ok with the Pertronix system installed and distributor one tooth off?

 

Shouldn't have made any difference at all. The Pertronix is simply a trigger and doesn't affect timing at all. Sounds like something else was going on. Maybe the advance weights or vacuum advance wasn't working for some reason, timing was off, etc.

 

I don't have experience with Pertronix but can share some experience with other conversions. The trigger event may occur at a different relative location with Pertronix and the points. Adjusting the distributor corrects for any differences. Can the Pertronix be installed out of sync for the odd-fire timing?

Being 1 tooth off shouldn't matter if you can still rotate the distributor enough to set the timing (been there, done that).