Injector balance. You have to find a shop with the necessary equipment to do this. The injectors are closed until injection pressure is sufficient to unseat the needle's spring pressure. As the injectors wear or are gummed up, different pressures are needed to unseat the needles and therefore, some cylinders don't fire.
The governor is trying to keep idle speed constant but it is impossible for the governor to compensate these cylinders, instead, the next injector gets a bigger swig of diesel, making that cylinder run stronger. The governor then cuts back fueling, causing another lope.
You could take the injectors out and give them a cleaning. Pro Shot Copper Solvent IV, available at good gun shops, readily dissolves injector goo. It works better than any other solvent.