Ok here is something I just have to ask.
You are running 2 12's for bass however you are using the headunit to power your highs. I can only imagine that your bass(when everything was working) was wayyyyy louder than your highs. Now you said the bass is not there like it used to be, well it is there but faint and distorted.
Any chance you blew your speakers??????
My guess is, and again this is just my guess:
You were running the highs with what, maybe 12 watts RMS from the head unit? Depending on how you had the subs wired anywhere from 400-1000 watts to the 12's. I think you were turning the volume up on the head unit too much trying to get the highs to equal the bass and blew the speakers.
How easily can you access the front side of your interior speakers? If you can get to them easy with the system off push the woofer in, if it feels stiff and gritty and does not go in and out smoothly then you blew your speakers. More than likely your head units amp was clipping and killed the speakers.
Next for the subs do the same thing, push on it and see if they slide in and out smoothly, if not you know what happened. If they do you really need to find an external music source to test them. I use my iPod, get a cable with RCA's on one end and a headphone jack on the other end. Hook it up and press play. If the subs work like they should then your problem is either your head unit or your RCA cables.
To eliminate the RCA cables, get another RCA cable that you know is good. Pull the radio, disconnect the ones you are using now and just run the new ones from the head unit to the amp. If the problem is still there you know it is the head unit, if not then you know it is the RCA's.
Now if the problem with the subs persists no matter what you do you have to test them seperate from the amp. Normally I would just hook them up to my home stereo reciever and see what happens. If you don't have access to a home reciever try and see if maybe a friend with a working system will let you hook up your subs in his car real quick to see what happens.
There are only so many parts in a car stereo, this is not rocket science.
Here is the steps I would take address the subs first and before you start to isolate the subs issue I would disconnect all the interior speakers that are hooked up to the head units internal amp:
1.) Hook up external music player to subs and see if they work. If it works, go to step 2, if it dosen't skip to step 3 (This step will eliminate the speakers and the amp if it works, leaving only the head unit and RCA's as suspect; if it does not work it will leave the amp and speakers as the suspect)
2.) Hook up a known to be good RCA cable in place of your existing one. If it works change out RCA's if it does not work change out head unit.(This step will eliminate the RCA's and if the problem is still there leaves only the head unit)
3.) Hook up subs to an external amplifier that you know works. If it works replace amp, if it dosen't pull the subs from the box and check all wires and connections including tensile leads from the voice coils to the binding posts. If all the wiring is ok then replace subs.
Now your bass issue should be solved lets move onto the highs:
1.) Press on the speakers to see if they are blown, if they are blown then find a refrence speaker that you know is not blown and hook it up to the head units internal amp one channel at a time and see if you get full non distorted sound. If so simply replace all of your internal speakers and call it a day. If they are not blown replace head unit as the internal amp is screwed up.