It might be due to the fact that your base stereo woofers are getting too much power. When i had them, i always had my XD gains low on them. I could never understand why the OEM Alpine upgrade didnt replace the woofers and powered the original ones with 80w.
It might be an idea to source some second hand L7 woofers. They are bigger but will fit in your existing enclosures. Some people have done this and have had good results, as they are bigger (8") and can handle more power.
Why was your HU replaced?
Turbo Dynamics Hybrid Turbos, Wagner Intercooler, DPF Delete Pipe with Sports Cat, Ecotune custom map ~ 422bhp & 618ft.lbs