rh:

1) Why the nine month hiatus? [This is a question, signaled by the use of a question mark at the end of an interrogatory sentence.]
2) To return to your initial post of January of this year, what was the running condition of the engine prior to installing the Pertronix? Why was the decision made to install the Pertronix?
3) Inasmuch as there is neither mechanical, nor electrical connection between the ignition system and the fuel injection system, the change to the ignition system should not have any influence on the injection system. [This is a declamatory sentence, ended with a period.]
4) As you describe the situation, the loss of half the injectors is associated with the closing of the throttle to the idle position. The idle position is detected by a switch on the throttle body. Look for a fault in either the wiring harness, or in the ECU, that involves the idle position switch.