When you are stopped (at a red light for example) and you depress the clutch, and then put it in and out of gear, does the idle speed increase when you put it in gear? Even a small amount, like one needle width on the tachometer?
If so, you probably have a bad clutch switch. Not the one at the bottom of the clutch travel that prevents you from starting until you depress the clutch, but the other one at the top of the clutch travel. The ECM uses the "upper" clutch switch AND the neutral switch to determine when the truck is under load and then modulates the IAC valve as necessary. So if your clutch switch is bad, then the ECM thinks that the engine is under load anytime the transmission is in any position but neutral (even when the clutch is depressed.)
Here is the logic that the computer uses.
Clutch Depressed + in Neutral = Engine
Not Under Load
Clutch Depressed + in Gear = Engine
Not Under Load
Clutch Released + in Neutral = Engine
Not Under Load
Clutch Released + in Gear = Engine Under Load
So with a bad clutch switch, the ECM will think the engine is under load ANYTIME the truck is in GEAR.
Another thing to look at is the bumper stop pad on the pedal. They can slowly wear a depression in the middle where it contacts the switch. You might be able to adjust the switch but if that depression is deep enough, you'll need to replace it or rig something over it.
Here is the stop pad:
Since it's only stumbling/stalling while it is in gear, that indicates that neutral switch is probably functioning normal and the clutch switch is the culprit.
Here is the procedure to test both the neutral switch and the clutch switch. On the clutch switch, you'll probably need to have a couple of leads with female spade connecters in order to check for continuity with it installed. You can always take it out and test it, but if you have that depression worn in the stop pad, then it might test OK on your bench but not be opening the contacts when installed. If you see a depression there, you might tape a penny over it for testing purposes and see if the switch is opening when the clutch is released.