Call Tom Langdon and see what he advises.
I have that set-up and it has been 100% reliable, with no adjustments needed.
How did you set up the choke?
I went through two new airtex fuel pumps before getting a good one.
I took some bad advice (from here) and tried a fuel pressure regulator (unnecessary with an original 4-7 psi fuel pump).
To be safe, I put on two fuel filters, one in the supply line and one at the input fitting on each carburetor.
The Pertronix unit seems an unlikely cause of the symptoms you descibe.
Why would it affect only one carb?
Why would it affect the vacuum advance?
