We are saying the same thing. When your engine hiccups/sputters your injection pump is loosing fuel pressure momentarily.
Fuel also cools your pump. So over time your pump wears and heats up. These injection pumps have very close tolerances and can suffer a catastrophic failure due to a number of variables that have to do with the loss in lubrication.
Loosing fuel pressure is something you can look into. Maybe it will cost you nothing if you just need to tighten up those bolts and do the work yourself. After all, most of the effort involved has to do with entering the engine bay through the bedroom and the owner is often more qualified than the mechanic.
Adding fuel additives (PS-Diesel or Howe's) at every fill-up is a good idea to help lubricate your injection pump. Note: I use to use Howe's because it's cheaper, but I changed over to PS-Diesel and every once in a while I will use Hot Shot fuel additive.
And you can install a FASS or AirDog to provide positive fuel pressure... worth every penny to avoid a break down on the road and an expensive tow.
Keep in mind all pre-2006 engines were not designed to run on USLD fuel. That means less sulfur in the fuel, and sulfur is a good lubricant. And there is nothing you can do about that now. However, using Bio-fuels are reported to have more lubricity vs. #2 Diesel without 5%-20% biofuels.
I have no problem using bio-fuels in my CAPS injection pump for this reason. However, a lot of owners mentally object to this stuff, because they heard from someone, who heard from someone else, to be on the lookout for "bad diesel fuel."
This is a holdover "wife's tale" from all our experiences driving cars. And those of us with Harley's know you can get bad premium fuel (low octane) that can cause our engine to stall out because the electronics sense the hiccup and that causes problems. ...But diesel fuel is not the same as gasoline.
Much has been written about this. You should search www.irv2.com
for how and why you should install a FASS or AirDog.
Your engine is always talking to you; and my advice to pay attention to what it is saying!