I could be wrong, but I think I'm seeing a bit of results from this work. Obviously, my system was a dirty mess, so that has to count for something.
But over the past two days, the vehicle has gotten quieter. As I've said before, I've suspected that some of the issues I've been having are due to fuel in one way or another. I think air was getting into my system and causing a clatter. I used to notice that it would run 'quiet' like this when I ran B20, I'm now running 100% diesel, and to my ear, it seems quieter than ever.
Over the past 30 miles of driving, I think it is purging that air. I'll be replacing the filter tomorrow (I wanted to let the old filter run to catch any muck left over from the old system before putting a new filter in) and I'll make sure to purge the filter well, then note how it runs for the rest of this tank full.