The big knob is the a/c idle up adjustment. It sets the idle speed when the a/c is running so as no not bog the engine down. Usually set it so the RPM comes up 100-200 RPM when the a/c kicks in. Should have no affect when the a/c is off. IF it does, check the plumbing there and see if the VSV is stuck open:
- http://www.4crawler.com/4x4/CheapTricks/22RE_Engine_Pix/13.html

Not uncommon for high output alts. to put out less voltage/current at lower RPMs. Sort of the nature of the beast, stock alt. comes up to full capacity at fairly low RPMs but the magnetic field saturates and that limits the max. output. Higher output alt. would have fewer windings of bigger gauge wire. Bigger windings = less resistance and more current (good) but fewer windings = less voltage at a given RPM (bad). Advantage is the output keeps climbing at higher RPMs while the stocker would level out at some point.