I have a 2000 F350 with the 7.3 Powerstroke. When I first start it, the "Service Engine Soon" light comes on and it runs really rough. Sometimes it will run OK when I first start it, but as soon as I hit the footfeed, it falls on its face and the light comes on. Around town, it stays on and runs crappy. If I get on the highway, after a few miles it may "plane out" and the light goes out and it runs like a top. Fuel pump or pressure regulator? Or am I way off base. No problem with it firing up.

 

The first thing to do would be to find out why the SES light is coming on, pull the codes.

Personally I am not thinking you have a fuel issue yet. Sounds more like worn injectors, or possibly loose UVCH(Under Valve Cover Harnesses).

 

Probably UVCH problem. If you keep driving it, it will just get worst. Try and plug it back in. You don't want to burn the pins in the harmness, you'll have to replace it then.

Chet

 

This is the video I usually post for people to watch to see what the UVCH 50 cent mod is. This is not my video but it is very informative. I fixed mine a few weeks ago and both sides were about 5/16" loose. I was probably only running on three cylinders. My truck was running just as you describe but when I started up a hill I had no power. You will need a SHORT 13mm socket and wobble or universal adapter to get the back bolt off of the valve cover. I used an air wand to blow the valve cover area down prior to taking the valve covers off. It took me 15-20 minutes to get the inlet pipe/tube to the turbo off and the intercooler pipe off the driver's side. Another maybe 20-25 minutes to get the valve cover off. Passenger side you have to use a bungee cord to tie back the heater hoses and you have the Engine Oil Dipstick attached to one of the bolts/studs. REMEMBER where the bolts go and where the STUDS go. Don't lose the special heater hose holders on the passenger side because they were 28$ each at the dealer(PO did not have one). Take your time. Hold the bolts securely. Digging for them without a magnet or flexible pickup tool really sucks.
The valve cover bolts are 96 inch lbs
The rocker arm bolts are 20 foot lbs
The lower Fuel Injector hold down bolt is 120 inch lbs
2001 F350 7.3L Turbo Diesel, UVCH - YouTube

 

Thanks! Looks like the UVCH route is the one I'll try.