What stereo? Does it have differential outputs? If not, then noise is to expect, since the power amp inputs are differential. You can work around that with filters, but it doesn't really fix the problem.

 

It’s a single dim cheapo with a small screen to the right. I got it for Bluetooth and back up cam. Not sure what differential outputs are though? Sorry, audio is not my forte! Lol. If this helps I clipped the rca plugs on the harness since there was no speaker rca plug ins on the deck. Used the 2 wires per rca plugs to wire up the speakers. Hopefully that didn’t screw things up! Besides the whining noise the sound is really good actually! I did ground the deck to the drivers side foot panel area but haven’t tested it out yet, did a inline thermostat abs waiting for a inline temp adapter before refilling the coolant. Can’t start it yet!

 

The stock power amp inputs use two signal lines (signal and inverted signal). The signal is differential and not referenced to ground, which makes it immune to ground loop noise. RCA plugs mean the signal is referenced to ground (since the shield is connected to ground). When you connect the RCA plugs directly to the amp inputs, one signal of the two inputs of the amp is connected to ground, which can cause noise.
Another workaround is to convert the unbalanced (RCA) outputs to balanced/differential, e.g.: https://www.ebay.com/itm/131703983966
This solution needs a positive/negative voltage source and you must be able to switch it on/off.