I was a diesel mechanic in the Army for eight years and worked the civilian side of the house for an additional six years.
Did you crack open (unscrew) the fuel lines to the injectors a couple of turns to bleed fuel in the lines? I'm not familer with John Deere engines, but the engines I worked on in the past needed the entire fuel system drained and bled if you get gas in the fuel. If there is a fuel pump in the fuel tank or fuel line between the filters and fuel tank, the lines should run from the tank or pump to the filters, then to the injector pump, then the injectors. There usually is a return line from either the filters to the tank or from the injector pump to the tank.
First step; drain the tank and refill, and drain the filter housing and change the filters.
Second step: turn on the master switch or ignition switch, but do not start the engine. Crack open the fuel line going into the injector pump until you get clean diesel fuel.
Third step: bleed the injector pump per the owner's manual.
Fourth Step: Here's where there are some differences. Bleeding depends on the engine maker because there are electric injectors, mechanical injectors, and injectors that operate via the fuel pressure timing from the injector pump. Your owner's manual should say how to bleed the injectors.
Your problem may be there is either air or gasoline in either the injector pump's "signal" lines and/or the injector's feed line.