Sounds like you some how got some air in the fuel line, this would starve some of the injectors of fuel and the one that was still pushing fuel was trying to make up for the dropped cylinders.
Your engine will knock and smoke when this is happening, and you'd think it was about to come apart.
Once it was bled of the air, it ran fine. Your fuel filter may not be sealing properly and allowing air to suck into the line as your gen is off. Or a leaking fuel line caused by a loose fitting or bad hose.
These can be very difficult to track down at times.
Dan & Loretta, US Army Retired Aero Scout Pilot
2012 Fleetwood Providence 42P Class A/DP
Spartan Chassis, 8.9L Cummins 450HP