When I install a system I ground ALL components to the battery neg, NEVER to the body. ALso good practice to replace the battery to ground 6 or 8AWG wire with 4 AWG. Even the amps ground is 4 AWG or larger as required to the battery neg. I use a ground distribution block to insure all grounds are at the same point. Never had any noise from any source, alternator, blower motors, HID headlights, ECM. You might try a ground loop isolator between the radio and crossover or amp. Sometimes the antenna ground may cause noise, I used to get antenna isolaters from PAC (
https://pac-audio.com/) I looked on their website but can't find it. One other possibility, if the noise is coming in on the radio power line, perhaps use the radio power wire to operate a relay getting power directly from the power distribution fuse block through the relay. The radio will still power off with the ignition but have a clean source of power. Good luck,
Retired Trunk Monkey