Long story short, i rewired my HU because the person before me installed the last HU without a harness and just tied the wires together from the HU to the cars factory wires. Which i have no problem with. The highs were just sounding strangly distorted so i just ripped it all out and redid everything and the high's sound 100x better..But now my 3 12's sound like there HPF isnt working or something.. The bass is much more "middy" then it use to be on alot of music. It doesnt sound "bad" but it doesnt make every song "punch" like it use to.. Alot of the bass sounds higher pitched and more heard then felt. I have no idea what caused this. I checked the RCA's , Amp setting, HU setting, no idea =\. Dont get me wrong, if i throw on some beats they still knock pretty darn hard but like i said, if im not playing a track with really deep bass, they are not pumping out what they use to.
Well if you unhooked the HU then for sure you cleared all the settings, re check them, sub output is on and the volume, xover settings as well as bass and treble. I know you said you checked them but it would not hurt to get the owners manual out and flip through it, there might be some setting that you forgot about.