This is an overly simplistic guess and may have nothing to do with your problem.

Our generators like to be run, and to be run hard. Loading a generator with a couple of air conditioners doesn't even come close to loading it. Running at light loads eventually dirties up the injectors and cylinders.

The cure, if that is the problem is simple. Run the generator long and steady and keep adding load. If you can get it running smoothly as your loads are increased to a total of 60 or 70 amps it will clean itself up after several hours.

Any diesel engine that is idled or run at very light loading over time is going to stumble and may even shut down if all of a sudden it is loaded.