Cleanup turns to mess up. Need some help troubleshooting.

The choke diaphragm you see is the choke pull-off, used to open the choke a slight amount after the engine starts and prevent it form being over-choked. It uses engine vacuum to do this. If the engine dies, and the vacuum goes away, then the choke-pull off will move out; I'm not sure if it will pop out or just gradually move out. But, the question is if the engine dieing is due to the vacuum going away suddenly, or the vacuum goes away due to the engine dieing. You can test by sucking a vacuum on the hose to the pull-off by mouth and see if the diaphragm is not leaking and it moves in and out with vacuum.

Not sure what FSM section you refer to; your FSM is quite different from my '62! Section 8 was for engines in 1962....

Put your voltmeter on the blue lead to the ballast and see if that is a steady 12 volts or close to that. Then check all the ignition system connections from distributor to ECU to ballast. Getting late here....