I have the same coach, same engine. I'll give you a few thoughts with the caveat that I'm not a mechanic, just an owner who's gone through similar. There are wiser heads here who might be able to help. Having said that...
On my '04 Vectra with the ISC 350, there was only ONE fuel filter. The engine manufacturer gives the specs, but the chassis builder (with input from the RV manufacturer who's buying the chassis) add things like the fuel filters. Many other models with our engine have two filters, but as said, in my case just one.
In your post you mentioned you changed THE fuel/water separator, which leads me to assume yours is the same. And if you do a bit of Googling you'll find that the filter likely is after the lift pump. See this thread...
Motorhome Magazine Open Roads Forum: Class A Motorhomes: 2000-2004 Cummins ISC owners beware
I had a lot of issues similar issues (attributed to bad fuel) until I had my Freightliner/Cummins shop install a 2nd filter before the lift pump. Not a cheap fix but took care of a lot of issues for me. I'd suggest you have a good Freightliner shop look things over and get their suggestion.
Just my quick thought...