It's an interesting thread. Very complex!
But it can't explain the incorrect ignition timing advance of his van.
So I think that he has an timing advance problem.
Gobowiec, does your problem is new, or you alway got this problem?
Have you made modification, or it happen like that?
I suggest you to connect your OBD2 port to a computer and run a program than can tune your car. You can adjust your timing advance like that, by programming the PCM. It should correct your misfire problem.