So I took the dash apart further. The yellow wire does go to a sirus receiver mounted under the steering wheel. The way it is currently wired with the amp should technically work as all is powered by the red accessory wire. The red accessory wire had 2 volts even when no key, 12volts with key. Is it supposed to have current all the time?
Is there a different wire I could tie the blue amp remote wire into ? Could the problem be the amp itself sending current back through the remote wire? I feel like when the amp is hooked up and voltage goes back through the remote wire it is somehow activating the red accessory wire as well as the stereo. That might explain the clicking I hear in the key area. It also supplies constant power to the stereo allowing it to operate sans keys
That's kind of how it sounds just from listening to you describe everything. The only way I could tell would be to get my multimeter in there for myself. Here's where I would start to trouble shoot it. Unplug all of the aftermarket wiring from the factory wiring harnesses, then meter the wires in the factory plug that are supposed to be the red and yellow wires in the aftermarket wiring. See if the 2 volts disappears. That will tell you if it's the factory wiring or the aftermarket supplying the suspicious voltage.