Can you replace the stock Pioneer head unit with something else without screwing up the Honda Acoustic Feedback System?

Yes you can. Only the rear speakers are part of the system. There is a black box that the rear channels go to, this takes the stereo signal and creates an amplified mono channel that goes to the rear speakers which are wired in series. Each speaker is 2ohms meaning a total impendance on of 4ohms.

Many people upgrade the 6x9s in the rear and say they sound better but they are forgetting the main point of the acoustic feedback system. The fronts do the sound stage and the rears are woofers playing midbass and midrange frequencies giving a good sound stage. Adding better 6x9s will add tweeters to play the higher frequencies which in turn will drag the sound stage back and negate the whole point in the acoustic feedback system.

Is it only a certain number of head units that will work with it? Because I got a new head unit a while ago and it doesn't work. I was wondering if there was anything I could do cause I did quite like it!

its good and you get way more bass than you would otherwise but it does make it a little wooly.

strip it out. sound deaden your back shelf and fit some decent 6x9s and you will get much clearer sound.

imo

Other option in order to stop this i to place a set of cross overs in with the 6X9 running on the bass output. Good 6X9 will then cut the tweater as its being filtered by the crossovers and hence give more bass without affecting the sound layout!

Honest, got it in me car! but im gonna run another set of tweaters in the rear columns to make it a night club in there lol