The first thing to do is scan the truck and pull codes. Work from te codes to find the issue.
If the EGR system is intact, I'd suspect the EGR valve to be stuck open, preventing the engine from making boost because the exhaust is just getting fed back into the intake. They run like dogs when the valve is stuck open, no power, won't shift.
The valve is on the intake manifold adjacent to the oil filter, one electrical plug with three or four wires, and three 8mm head bolts holding it down. If it's got a lot of carbon buildup, it takes some prying to get it out, be gentle though an you can reuse the gasket and o-rings. Carefully remove the o-rings once you get it out, clean it up really good, inspect it to make sure both seats are seating fully, reinstall the o-rings and let them rest (shrink back to size after stretching them to get them back on) and then use a light swipe of oil to let them easily slide back in, bolt the valve down and it should drive fine.
Start with the codes though. If you can't pull codes, then I'd suggest checking the EGR valve, when mine stuck open, it was running fine, I parked the truck for a couple hours, went to drive it and almost got T-boned turning onto the highway, when I had enough time to make that left three times over if the truck had been running normally.
If you want to be proactive, get an EGR valve gasket and o-rings before you pull it apart, then you don't had to reuse anything.
The Current Truck (Oct-2013 to Present):
1999 (Early) F-350 Lariat, CCLB, SRW, Black/Tan
7.3L Powerstroke, 4R100, 4x4, 3.73, 37x13.50-18s, '05 Axle Swap, 6" Fabtech lift, GTP38 "D66" turbo upgrade, SCT 4-position chip with custom tuning by me, Straight Piped 4" down pipe through 5" dual stacks, N-Fab full length triple steps, Pro-Tech cab guard and tool box, louvered 5th wheel gate, Hella 500 Fog and Driving lamps, much more to come...
The one I'll miss, (Mar-2009 to Jan-2014):
2000 Excursion XLT 4x4
6.8L V-10, 4R100, 4.30, 285/75-18, 271whp / 388wtq
The one I won't, (Jul-2005 to Sep-2012):
2005 F-350 XLT, CCLB, SRW, 4x4 FX4
6.0L PSD, ZF-6S650, 3.73, 35x12.5-18, 4.5" Lift