OK, I have the Bentley Manual here and it says the idle speed is via the Idle Speed Control Unit and Idle Air Stabilizing Valve. So I think your on the right path.
The ISCU has multiple inputs such as: coolant temp., air temp., engine speed etc.
If for instance the coolant temp. wire to the ISCU is loose the unit might think the engine is not warmed up, or the sensor could be faulty.
Idle speed is not a function of the main computer.
If you have a manual, you'll be able to go through the steps. If no manual it would be very hard to find the problem if it was'nt something obvious.
02 GMC Yukon SLT 5.3
02 Ninja ZX9R