Pull codes.
Your truck doesn't have a CEL.
I already replaced the fuel filter and have already removed and cleaned the AIC and the EGR valve.
Is that the right connector?
Is there any change when you unhook the IAC while it's running? My spout was a little "pill" off of the injector harness, more like a small square. You know you have it when the timing doesn't jump around all over the place when you have the light on it. The SPOUT bypasses the computer's ability to adjust/tweak the timing. It will stay at a solid 10 BTDC (or whatever you're timing to). It's basically like disconnecting the vacuum line off a vacuum advance distributor.
Specs call for 850 RPM but she insists on going back to 1000 or so when driving. If I lower it more the engine won't idol smooth.
Spray carb cleaner around all vacuum lines, and between the lower and upper intakes. I had a vacuum leak develop between the last runner, all the way in the back. I thought an injector wasn't sealed at first when this happened to me. I had reused the gasket though. High idle and popping were my symptoms. I could hear it hissing, too.
Is the FPR the item to the rear of the engine, Close to the firewall on the drivers side with lines hooked to it that clicks or buzzes during engine run?
It's on the fuel rail, near the firewall, drivers side, but it shouldn't buzz or click. What you're probably hearing is the fuel pump relay (click), ecc relay, and frame mounted pump (buzz) under the cab. You also have a fuel pump in your fuel tank. Check the vacuum line for raw fuel, if you do, then it's allowing fuel to enter the engine through that vacuum tap. Best way to know if it's a fuel problem (too little or much pressure) is to check with a fuel presure tester.
Does it run rich cold? If only warm, could be a bad O2. Running rich can clog a cat.
When you indicate that it's putting out fumes, is it blowing black smoke or anything like that?
Did you move the "idle" screw on the throttle body at all? The computer is what controls the idle, that screw on the throttle body sets the base line resistance/voltage for the sensor. If so, you might want to re-adjust since that might make the issue a little more difficult to diagnose.
Finally, since it's running rough verify that none of the wires are cracked (look at the engine (don't touch) in a really dark garage while it's running, look for them arcing to ground), check condition of your plugs, and a compression check might be a good idea if you run out of ideas. Vacuum gauge will say a lot about the condition of your engine as well.
Pete