When I changed the manifold on mine, it took more than 10 cycles of the key to clear out all the air so the engine would run smooth. I would imagine that the recommended 3-4 cycles isnt cutting it for you either.

When you cycle the key, listen to the pump. You will hear the pump go thru its run cycle and will be able to hear the air bubbles in the fuel. Listen for the complete cycle each time and continue to cycle power until this is minimized.

This cycling is how to bleed the system.