The IAC is a posibility, but keep in mind that the clutch cancel switch signals the processor on these trucks and it will affect idle, as will engine temp. (I've seen some problems with after market air intakes and filters causing this type of problem).
I would do a computer scan first, also be sure there's no codes and that the throttle body and IAC are clean, and that the base idle is set properly. Also make certain that the engine is reaching full operating temperature, a stuck thermostat will also cause an irratic idle. Idle is kept slightly higher when in gear and driving for both emissions and drivablity purposes. Stepping on the clutch or shifting to neutral both signal the ECM that the engine is no longer under load. The clutch cancel signal is used for this as well as the canceling of cruise control on some vehicles.
From your description, it sort of sounds like maybe the IAC is not working or that the throttle body is dirty. Both of which will reduce true base idle and let the RPMs drop below spec when the ECU calls for a minimum idle.
If it were mine I would first scan it for codes and check the airfilter and throttle body.
The IAC can sometimes be cleaned, but cleaning won't fix one that's simply quit working. The MAF sensor can be cleaned, but the actual element is very fragile, it sort of looks like the filament in a light bulb. You can clean it with MAF cleaner in a spray can, or if your super careful, some alchohol on a Qtip. I would also make sure that the air cleaner is clean as well, this can also affect idle quality