I do not personally liike the way this going for you. If the fuel tank does not have an obstructed vacuum relief line. I am going to assume you have been testing with the cap loose or off? Stuffing a rag in the neck stops most fuel slosh out if tank has any amount of fuel in it by the way. Retained and building tank vacuum over a few days would cause major problems. Just removing the cap now when idle is rough. Idle should restore in less than five minutes if the vent is closed.

Other than that you only have one test left. The totally independent fuel supply source to the pump in my opinion. Normally the pump should clear itself of air once running if in good shape. Plus stay clear of air. For a better opinion on this others should comment that have or have owned your engine type. I do not know it all. Or if you do an absolute test and problem remains Talk to an injection pump place.

One last thought as well. As system was using alternative fuel previously try running the injection pump on it. If problem leaves pump may have excess wear internally. I hope that is not the issue. Probably not in fact but no easily turned stone should be ignored.