Although this may not have any bearing on your problem, I would offer the following thoughts:
1) What are you using to lubricate your fuel system?
The reason I am asking is that with the ULSD (Ultra Low Sulfur Diesel) your mechanical pump is not getting the lubrication it did with Sulfur in the fuel as it was 10 years ago. While there are a lot of differing opinions on this topic, I believe our pumps are operating at a disadvantage because of the ULSD and this is problematic for the entire fuel system. I have read studies that compared original diesel to the current product and then proceeded to compare the old fuel against the new with additives in the fuel. To make a long story short, here is what i do to "feed" my deuce.
I add 1.5 ounces of 2 cycle oil to each gallon of fuel. Originally, I was adding roughly one quart to a tankful, but have upped the addition of the oil as it seemed to make a big difference and I felt I needed a little more. So far all is well. The Multifuel will burn the oil happily anyways if for some reason it is too much.
2) I also add "POWER SERVICE" diesel fuel conditioner which has a cetane booster and also other additives that improve the flow of the fuel and prevents gellling. Not sure how much this does, but I have done this since I got my truck at the advice of "JATONKA" who is one of the "Deuce Sages" on this site and if he says do it, I do it, simply because I know he has probably forgotten more than I will ever know about my deuce.
It is possible your injector pump is suffereing from the low sulfur fuel and a shot of oil in the fuel may help. I also know that in the injector pump some other issues can crop up that are not specifically fuel related.
My suggestion in summary is to get as much support from all of the folks here and then you may want to try some, or not, but at least you will be working with more ideas than you have now.
Best of luck and I hope things work out easily for you!
RL