Make sure you are not processing a lot of air at times. A clear hose on the return output of the pump if yours is too dark to observe is a good ideal. An air leak can be intermittent in nature as well.

Usually it is also good practice to change out the fuel filters on suspicion especially if the existing ones have been on a long time. Make sure the injection pump is flowing return fuel into the return line is important in my opinion.

A hot injection pump from lack of the cooling effect of fuel exiting the relief valve might cause a real reaction from the injection pump. That's if its operating temperature has risen substantially above normal. Say on a highway run is a good example.

All the time when those internal pistons are compressing fuel they are building heat. High enough retained heat and even the fuel might boil in there. If that where to occur the engine might run as you describe.

Someday hopefully I will temperature scan some pumps with and without the overflow functioning. After a highway run. At this time what I am thinking is not scientific enough in nature. Still there is some possibility.