There are two idle control systems on the 3.0.

The most known one is the ISC circuit, a stepper motor with a sealing plunger that modifies an orfice opening in the TB, controlled by the ecu. The second FIdle system is a mechanical wax pellet capsule type that controls the first few minutes of idle, raising idle speed on first cold startup for emissions control, and it can only be fixed with a new TB. I think that one is ok on yours, because you get a higher first start idle that comes right down.

I suspect one of two things.

First, somebody has messed with the idle stop screw on the main butterfly to "fix" and idle problem caused by a bad ISC in the past, raising the mechanical base idle speed, in which case you have to do the fsm base idle speed setting they say is not necessary (so why do they tell you how?). This is fairly complicated, and also requires resetting the TPS/IPS so it reads proper throttle idle position and open position.

Second, you have a vacuum leak beyond the capability of the ISC to compensate. Look for it by sound on an idling engine using a piece of vac hose in your ear. You can hear the hiss easy that way, and localize it. Scan the end of the hose around (it's very directional) and you'll home in on the source.

There is also an air bypass screw on the top of the TB, perhaps under a cover, down in a hole. Try adjusting that to curb idle speed after warm up. Since that's the easiest, I might try it first.