One of the first things I noticed when I joined this forum (I am from TCCoA) back when I got my 94 Mark VIII Base earlier this year (build date was mid to late 1993), was that I had talked to numerous people who were very connected with the stock JBL system in their cars..
I am not saying that you are one of these people that are insistent on keeping the JBL setup, or even part of it; I just thought I would mention it because it seemed funny to me!
I really think just throwing in a modern head unit with really good aftermarket speakers (wired directly to the head unit) sounds even better than the full JBL setup if the install is done right. Years ago I had a friend with a 95 Mark, who used the stock JBL system, but added a mono amp and digital crossover to the trunk to run a single 15" sub, and it sounded pretty decent considering he had used no-name crap parts to build it...
When I got my Mark, my stock JBL head unit didnt work along with almost everything else in the dash as well, lmao.. no radio, and it would not talk to the cd changer in the trunk. It threw some error code up on the little LED screen, but I dont remember what it said and didnt care because I have a custom built stereo in my garage (that I plucked from my Tbird) that consists of a digital Pioneer DIN sized EQ, full setup of aftermarket speakers for the cabin, 2 Kicker comp 12" subs for the trunk with a custom amp rack I made that mounts to the back of the box that holds cooling fans that turn on with the system along with all the relays for it, and 3 amps (almost 3000 watts total), and digital 3 way adjustable crossover. I added green leds all over my trunk and built the setup into the trunk where it looked like it was OEM, and took a title at a local car show for the "best audio system setup" years ago.. I built this system for very very cheap too with proper use of Ebay.. Lets just say I was glad I had my entire Tbird dynamatted!
I guess you could always "bypass" the stock setup, but life will be much easier for you if you just pull that rack in the trunk out assuming that you decide to upgrade the system with subs - not much clearance for subs if you leave that rack in, and you dont have to blow $25 on something that will just get in your way in the future.
So far I just threw a Pioneer CD player in the car, and I am currently running the stock JBL speakers directly off the head unit and while it doesnt sound too bad though its VERY weak! I still have to install the beasty stereo system in my Mark; but the point is that I didnt even want to deal with this JBL setup - I am sure I could have found the issue and fixed it, but it just wasnt worth it to me.
I suspected the amp was the issue, but I was told that the head unit and/or cd changer most likely was at fault. Because I never installed my subs or anything else in the trunk yet, that PIA amp rack is still in there with all the original hardware along with the cd changer...
Do you want my old hardware from my trunk if it proves to be a match? I am not sure what works and what doesnt, but this JBL equipment is easily repairable from what I heard. Ill pull down my amp rack today or tomorrow if you are interested and Ill get some pics of everything. You can have all the goodies, or just the amp if you want for only the cost of shipping so let me know when you have a chance!