I'm not the expert here for sure, but I had terrible problems with a Pertronix Ignitor III, said my piece many times. They are (or were) badly made mechanically. The top plate on mine was seen to be moving around and likely shorting itself out while on a distributor machine,
During my ignition wows, I did as Don suggested, went back to points, BUT if your resistor wire is bypassed, you'll need to add an appropriate resistor. I forget exactly what I used Ohms wise, but it was like the Chrysler type that I temporarily screwed to the firewall. I also used my stock coil. With the points, the motor ran great, proving the P III was bad. Pertronix replaced it with a P II and coil, and never had a problem since. Other than I rebuilt the distributor to allow only 20 degrees on crank timing. I found on my '71 4V, 16 degrees of initial is just about perfect. It is a matter of trying this and that sometimes.
As for fuel issues, even though you have a clear filter, (hope it's not glass!!) I think you could still have a blockage somewhere. Does your carb have those porous metal type (can't think of the name!) in the inlet passages? They could be partly plugged. Again, relating to my own issues, while my engine did not die, it was running rough, sputtering etc. Finally I changed all my fuel delivery system. It proved to be a combination of rust in the lines, rubber sediment likely from the use of Ethanol fuel before I bought the car. So after that, no more issues.
Bottom line is there is so many thing that affect the running, it comes down to eliminating one after the other, including ones own FRUSTRATION!
Hope you get to the bottom of it soon,
Geoff.