check engine light runs rough. idles rough.
 

96 powerstroke 7.3 220,000 miles. has a bully dog programmer hooked up,not through the obd port its hard wired under hood next to the fan motor.a/c inlet shroud. water was in fuel,i dropped the tank and thoroughly cleaned it. disconnected fuel lines and from lack of compressor i gravity drained the fuel lines.had to replace injector harness on passenger side rear harness, (my truck was vandolized and disrespected)it had been cut. i replaced the cam position sensor today, no change. please help

So had water in fuel, you cleaned fuel lines and tank(s).

Replaced passenger side rear harness? the one under the valve cover?

CPS wont cause a rough run, it will cause run or no run.

Is it sounding like its missing and shaking really bad, or just sound like its running rough? You still might have a injector harness issue.