I have an RPM specific "click" when listening to the radio. Not a relay, but the sound is RPM dependent. Not sure if the radio is picking up the ignition, injectors...something else?

Could this be a symptom of a bad ground? The HU is a Pioneer. The noise isn't there with a CD, which makes sense.

Any ideas?

 

Seems to me if it were a bad ground you'd be getting the clicking all the time. When you say it's not there in 'non-CD' mode - you mean with the AM/FM, right? If so, I'd start by looking for something exposed or making contact in the antenna circuit....

 

Check the ground on your eng & batt. You are hearing the sparkplugs fire. Have you changed sparkplug wires recently & what kind are they?
Do you have a volt/ohm meter? If so you can also check the antenna ground.
Where is the ground on you radio? If you used the ground wire in the harness that could be a problem in a Toyota the radio needs to be grounded to the chassis.

 

On my pioneer HU, I can hear the engine wind up through the stereo when I put the stereo into aux input mode, and my aux device is off. If I were hearing it during radio or CD play like you were, I would install a power (or ground) line filter in the stereo wiring. I think you can pick them up cheap at Radio Shack.