I'm trying to isolate some of the noises and rattles in my car. Part of my problem is the RCA plugs from the 90BT harness that are not being used. I'd like to remove them from the connector completely. Will this affect anything if I pull the unused RCA wires from the white harness connector that goes to the radio?

except your hardware bypass and remote system (or maybe radio amp control) turn-on, there is nothing essential in this harnass

I would mark down there locations in the adapter and/or take some pictures, and carefully remove the unused ones just in case you need them down the road.

it might be better if you secure said RCA plugs to the harness (by means of a velcro strap or a zip tie). Just a basic wiring idea, not just specifically for car audio, but for anything out there, including the unused power leads inside a computer tower.

Removing the RCA might mean down the road you'll have to reattach them when it turns out you need them. That's more work compared to yanking the velcro strap or snipping the zip tie.