Are you getting the engine overtemp light with the high idle as well? From my research that means the boat is in "limp mode"
With a little more troubleshooting last night, we isolated the problem down to a couple parts. We would turn the perco off to let the computer reset, and on startup, we had no light and normal idle. My RPM gauge doesn't work so I can't tell you what it was idling at. When we throttle up in neutral or drive we get the light, and when we throttle back down, the idle is high.
Fuses are all good on back of motor as well as the relays.
Checked range of motion with throttle while watching the cable on the motor and it travels normally.
You bring up a good point, when we have the light with high idle, the throttle doesn't respond in drive until it's almost parallel with the deck. WOT is pointing at the floor. When we had no light, the throttle seemed to respond on a much shorter throw until it tripped the light.