If they really did run a compression test and it came back OK, then you can rule out things like bad piston rings, leaky head gasket, burned piston, scored cylinder wall, bad valve or valve seat, etc. In other words, most of the things that would force you to pull a cylinder head and/or get a machine shop involved.
So with Compression out of the picture, you are looking for Fuel, Air, or Ignition issues. (Just assume for a little while that emissions and engine control sensors and whatnot are not the problem--since the PCM monitors those things, it *should* spit out a trouble code if they are malfunctioning. Yes, it's possible to have something fail w/o a code but it's a long shot so don't chase your tail on that possibility yet.)
Air - Keep looking for vacuum leaks. One area that is often overlooked is the vacuum hose leading to the Fuel Pressure Regulator. It's not usually a problem, but I have seen them fail with almost-invisible cracks that could only be pinpointed by removing the hose, plugging one end, and applying vacuum to the other end with a vacuum gauge. Your truck is fairly new so I'd be surprised if that was the culprit but it doesn't take long to check and then you can move on. Other than that one, keep looking in the usual places (i.e. any vacuum lines connected to the manifold, check intake gaskets, etc.) Look for burned or chafed wires, or poor connections leading to the MAF sensor, TPS, and IAC.
Fuel - Add DryGas if you haven't already. Change fuel filter if you haven't already. Check fuel pressure. Other less common problems are obstructions inside the fuel rail (I have seen pictures of flaked-off chrome from the fuel rail settling in and clogging an injector. This one is particularly nasty as it can move around from one injector to another, and be just enough of a nuisance that it doesn't set a code.) I think you would have noticed that when you cleaned the injectors though. Check the fuel system wiring for signs of chafage, burning/blistering, etc.
Ignition - I think I have my stock ignition coil sitting around. I'll have to check if it works for your '03--if it does I'll mail it to you and you can swap it in to see if it makes any difference. You already did the plugs and wires so that's everything on the high-voltage side. On the "trigger" side, the cam position sensor and crank position sensor typically throw codes as soon as they become a problem, but keep them in mind if other troubleshooting doesn't fix your truck.
The one service that I *would* consider going to the dealer for, if all else fails, is a cylinder load balance test. (It's pricey but when traditional troubleshooting fails to produce results, it could be cheaper in the long run than doing all this labor and replacing parts when you don't really know what's up.) For the test, they run the engine under load and shut off ignition & fuel to one cylinder at a time and observe the effect on the engine's output. For example, if shutting down cylinder #2 has less of a negative effect than shutting down #1 and #3-6, then #2 obviously wasn't providing as much output as the other cylinders. Then you can look for ignition or fuel problems specific to that cylinder. But if you already did a compression test, and replaced the plugs, wires, & coil, and checked/cleaned the injectors, there really aren't too many more options that would be specific to one cylinder.
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I have seen other components mimick engine problems. One guy in my SHO club had a bad torque converter clutch and it felt exactly like a misfire. It didn't throw any codes for thousands of miles and he ended up chasing his tail on that one until the problem got bad enough to throw a code.
