Isn't idle controlled by the ECM on your (TBI?) injected motor?
It could be caused by a faulty sensor (maybe ECT?) but I'm thinking you might try swapping the Idle Air Control valves to see if the issue follows the parts. If you do that don't give in to curiosity and push or pull the pintle plunger. And let it run a bit while the ECM may be re-learning IAC reaction to it's "commands".
Does that ignition require setting base timing?
And also suggest clean (wipe) out carbon in the throttle body at the throttle plate ( both engines) and be sure the flame arrestor is pretty clean.
Lastly , make sure the helm controls at idle ( especially on the higher idle engine)back off the throttle cables with a little slack so the throttle plate closes and TPS throttle position sensor goes back to 0%.
(FWIW- My blue 5.7L MPI engines have ECM-controlled idle RPM at 640 on warm engines.And base timing and advance are fully controlled by the ECM, not user adjustable , though the critical Cam Retard Angle is adjustable by turning the dist. base with help of a marine scan device to read it. That last may not apply to your TBI engines. )