[DaveO430]

Probably something still not right in the carbs or have you verified the ignition system is working properly? The points and timing are critical to it running right.

 

[DaveO430]

The original carbs had an intermittent fuel related problem, the 1100 carbs have an intermittent fuel related problem? Is it possible it never was fuel, but timing/electronic ignition?

Exactly, there is no reason it would not run well with 1100 carbs. It might run differently but still should run evenly. I have worked on a couple 1000s with 1100 carbs and they ran just fine. Have one out in my shop right now. If you are sure everything is copacetic in the carbs look elsewhere.