I bought a 1999 F-350 a little over a year ago. I too it to jiffy lube for an oil change. After the oil change it started to run rough and had a lot of rapping and tapping comming from the top front of the engine I thought. I replaced the idler pulley and the tensioner. Some of the noide went away. the truck still ran rough. After asking for help in the main 7.3 forum I ended up here. I drained the fuel bowl 2 times and refilled it. all the noise has gone away but it still idles rough. I have only driven it 12 miles since doing this. Does anybody have a scanner that lives close to Augusta? There are no warning lights showing on the dash.
Your problem reminded me of the time I had the oil changed in my 94 7.3 work truck. when the service man refilled it with oil he stuck the filler nozzle in the valve cover and broke an injector wire. It seems that the injector wires are made into the valve cover gaskets. Just a thought. Sorry no scan tool.