Rough Idle, reprogram truck to stock?

[86cucv]

95 F-350 Powerstroke, Auto

I have a rough idle issue with my truck that I am trying to track down. I first thought that the injectors may be at fault so I had Jim at rosewood rebuild them and the truck still has a rough idle. It basically feels like there is a miss between 500 and 1500 rpms. Above that speed the motor seems to smooth out and run fine. The truck doesn't hesitate and it has plenty of power, also no smoke or oil consumption. I changed the oil 600 miles ago with 15w45 rotella T and a WIX filter. I suppose the next course of action would be to check the fuel pressure? I took my truck to Turbo and Diesel Injection in Indy last week and had them run a few diagnostic tests on it. It passed all tests but the guy said the truck has a chip or tuner on it (Apparently the tester can pick up on that). Either way, if I do have a programmer installed (I just bought the truck last month, guy didn't know what had been done to it before he had it), is there a way to reprogram the truck back to stock to see if a program could be causing it?