I doubt it. I do not have a VSS at all and I have no other issues. My setup is on the engine that it was designed for though. You have such an odd combo of parts its hard to trouble shoot anything...

Some questions. What is your fuel pressure? What injectors? What EECIV manual (A9L) or auto (A9P) or something else? Is it a manual or auto tranny? Do you have a VSS wired in?
If you are...