I would go after the hydraulic head o-rings first. They like to flatten out over time. From my experience it has been the most common cause of fuel in the oil other than FDC bypassed.
If the FDC is not bypassed, do that first.
If the FDC is bypassed, replace the o-rings on the HH.
MY M109A3 was leaking fuel in the oil and my HH o-rings were flattened out. New o-rings and then I never had a problem after that.
Changing the seal on the boost pump is a pain. You cant get it out easily and I wouldn't go after that right away. I feel strongly on the HH o-rings. Your method of pulling the plug on the back of the injection pump is a good idea, but you would be there forever since the oil would be draining out and you might get fuel confused with oil and visa versa. It might be hard to tell anything from that. the seal on the boost pump is pretty much just a lip seal, not meant to hold any real high pressure. This video on youtube shows a guy pressurizing his boost pump to 60PSI with air and showing the seal leak... But i do not think that that is an accurate "real life" test to check if the seal is leaking. Lips seals are not meant to hold pressure like that. The correct test I think he should have done is to spin the shaft somehow like it would be in the injection pump and pump diesel with it. Then have a 60 PSI pressure relief valve so the pump is constantly pumping 60 PSI. That would be the exact scenerio that the truck would see and yield more accurate results.
Here is the video that I think is not an accurate test for the boost pump seal (just in case you want to see it)
https://www.youtube.com/watch?v=Q0gxynQiOU4