^^^ see above
OP, troubleshooting these engines often takes data combined with intuitive experience. With them being so electronically controlled, data from those controls is needed.
-If you have good fuel pressure, that's good. Dont need to worry about that.
-What kind of CPS did you use? The best reliability typically comes from a Ford or International part.
-Any check engine codes?
-Any hot/cold start issues?
-Is the issue more noticable when cold or hot? Is the EBPV still hooked up?
If you have a buddy with Auto Enginuity or a Scanner that can datalog, that would be excellent. If not, I'd be looking for a diesel specialist that can assist to get this data. Where do you live?