Hacked into amp/radio wiring

I decided to finally take a look at my factory stereo(Premium with GE)
Since I bought the car, it has been enough to get me by, but not without wanting more.
The drivers side speakers(dash&door) work, as well as the passenger speaker on the door. They don't put out a lot of sound. As a matter of fact until today, when I put my ear up to the drivers side door speaker, I didn't even know it was working, I thought it was only the dash speaker.
The rear speakers are not there at all.
I don't know the history of this car all that well, but I can make some pretty good assumptions I think.
First of all, when I bought the car, the trunk lid torsion bar was in the trunk. We wondered why it was out, but while reinstalling it we noticed a chunk of metal was missing out of the metal in the trunk. It seems pretty obvious that the torsion bar, the removed rear speakers and the hunk of missing metal were all to accommodate a big speaker box in the trunk.
I don't know what their intentions were. Maybe the sound system was fine before they messed with it, maybe it wasn't.
What I do know is that the speakers in the dash and door appear to be original, and the wiring behind the radio seems fine. The radio and graphic equalizer are both there and worked alright, until today that is.
Knowing what I already know about what's up front, it seemed like taking a look in the trunk would be a good place to start.
What I found is that the mounting tabs for the amp were broken, and it was just kind of floating in there. The wiring is definitely cut into. They maybe modified it to bypass the factory stuff, and then put it back together when they sold?
When I hooked speakers up to the rear connectors, I was getting a very quiet sound from both of them with the radio on. Checking them with my multi meter showed .02
I moved on to wiggling the individual wires near the amp to see if I would get any sort of reaction.
I definitely did. The amp, as I previously mentioned was not attached to that metal piece in the trunk. I bumped it while I was messing around, and the metal of the outside of the amp made contact with the metal of that piece it is supposed to be mounted to. I saw a small spark, and heard the radio turn off then back on again. Unfortunately I did not have anything back there to put between the amp and the metal piece, and I saw another small spark as I unsuccessfully tried to sit it carefully so it wasn't touching anymore.
I now have no radio at all. When I push the power button, you can tell it is doing something, as the lights on the GE turn on and off still with the power button.
I checked fuses 11 & 13, both which seem fine.
I would have rather not wrecked the stereo, my intentions were to find some bad speaker wiring and fix it and use the factory setup for now. But I was quite open to upgrading.
I'm just wondering, does anyone know what it is I have done? Why my radio is not working? I didn't really get far enough to determine if the wiring job was bad or not. The fact that the one speaker didn't work, and that I was getting such a low signal to the rear speakers seemed like a good indicator though.
I've been looking through other posts about the radio in general, and I likely will just upgrade.
I'm just starting from what looks to be an altered already, or maybe altered and restored condition rather than just starting out with everything original.
More for myself so I wouldn't have to hang out in the trunk to revisit what I saw, I shot a 30 second video showing the wiring. I'm going to post a link to it below, I'm sure it will be really obvious to you guys that have upgraded or simply know this stuff. To me it looks like a jumble of wires.

Hoping someone can point me in the right direction. More or less just wondering if the damage is likely limited to the amp or stereo itself and if I would be good to move on to replace it.
As I don't know what the original wiring looked like, I also don't know where to start. I've scoured the site looking for a guide that I have heard referenced several times in other posts I have read, it's supposedly in the FAQ. I can't find it anywhere.

This is a link to the guide

Rob,
That's a bummer about your wiring and how some people just get in there and cut things up to make it work, that kills me. I would start by looking over all of the wiring in the trunk as that is where most of the hack has been. I would be checking every wire for correct color to color and make sure the connections are good. If your amp sparked it would seem it is not grounded. I would re-connect every cut wire and solder them to ensure a good solid connection. Since your mounting tabs for the amp were broken, maybe some large zip ties will at least hold it in place. Best of luck

I've been reading everything I can on the subject that I can find on the site.
I am wanting to just move on and put an aftermarket head unit in and new speakers. If the wiring is good I might just use it, if not I'll run new wires.
I wish I could find the write up on how to bypass the amp. Is it a matter of simply disconnecting the amp in the rear, then using the alternate plug from up by the glove box? Or is there more to it than that?
If that was the case, could I just ignore that hacked into wiring by the amp?

^^^^ +1

I bet at some time the PO put in an aftermarket head unit, but removed it and put the stock system back in to sell the car.

2 ways to wire in an aftermarket head unit:

1) The WRONG way: Run wires from the aftermarket HU all the way back to the trunk and connect the new wires to the speaker wires coming out of the POS amplifier in the trunk. It looks like thats how yours is currently wired.

FYI, the premium sound amplifier puts out a huge, gigantic 8 Watts RMS per channel, which by modern standards is equal to zero. Even the cheapest POS HU from Wallmart will put out over twice this much power, and a good $150+ HU will put out over 5x this power. Most aftermarket HUs will have built in graphic equalizers with different adjustable settings for different sources (radio, USB input, aux input, CD, etc) plus "loudness" to automatically boost bass frequencies at low volume levels.

Example of even cheap aftermarket quality: A friend has a 10 or so year old BMW with their "high end" audio system. It sounds pretty good. I have a $50 reman Sony HU from Ebay, a $55 150 W subwoofer from Ebay and Wallmart speakers in my 95 Taurus winter beater. Total investment around $160. The cheapo system in the 95 Taurus sounds WAY better than the "high end" system in my friends BMW, and the higher end systems I have in my TC and 86 Tbird 5.0 make the BMW system sound like a transistor radio from the 1960s.

2) The RIGHT way: There is a second 8 terminal connector hiding in the dash in back of the radio that goes directly to the 4 speakers. FYI, dash speakers and door speakers are simply wired in parallel. If you go with aftermarket speakers, best to use a filter capacitor in the line to the dash speakers so no need to run wires back to the trunk from a new HU.

You are probably right about the previous owner. I have read that the other connector would have been by the glove box if it wasn't used.I have had the radio out before, and both of the connectors are back there.
So I don't have to do anything else? I can forget about that wiring in the back? What about the amp?
I don't know much about this stuff at all. I get what you mean about the speakers being wired in parallel I think. I don't know what you mean about a filter capacitor and not running lines to the back...

Is it as easy as removing the radio and GE, installing a new HU with the other non premium connector and that's it as far as wiring? When you say the other connector goes directly to the 4 speakers...do you mean the two in the rear and the other two go to the four front speakers with one door and dash speaker on the same connection?
I was reading an old post (Here)that mentioned disconnecting the amp, and I have heard MANY references to bypassing the amp...

Rob,
I put a JVC HU in mine last year using the $10 Ford adapter kit they sell at Wal-Mart. You have to disconnect the factory EQ up front and plug in the new harness connector. It was super easy and there is a write up here in the Technical section about it. That's what I followed and had no problems, but all of my factory wire was as factory and not cut. I also replaced my factory speakers with new Pioneers, sounds much better with my 25w head unit.

Rob,
I put a JVC HU in mine last year using the $10 Ford adapter kit they sell at Wal-Mart. You have to disconnect the factory EQ up front and plug in the new harness connector. It was super easy and there is a write up here in the Technical section about it. That's what I followed and had no problems, but all of my factory wire was as factory and not cut. I also replaced my factory speakers with new Pioneers, sounds much better with my 25w head unit.

I keep hearing about this write up in the technical section, or in the FAQ some other posts say and I would love to see it.
I'm going to feel pretty stupid if it's right here somewhere obvious. But I swear I have looked everywhere for this write up, it's either not here or I'm blind
If anyone knows who wrote it, or maybe the title, or a keyword I can search with...I've tried with no luck.

I printed out what I used for my install. Here is what it said;
1) Disconnect negative battery cable and remove original radio.
2) Open the trunk and remove trunk liners, cardboard cover and disconnect the 2 connectors for the factory amplifier, which is mounted behind the rear seat.
3) Remove glovebox at the piano hinge.
4) Locate secondary radio wiring harness which is stuffed up against the dash to the left of the glove box door right along the top edge where the glove box closes.
5) There are 2 connectors. Leave the grey one connected and pull the black one out for access.
6) Obtain a wiring harness adapter from WalMart, Kragen, Autozone, etc. Runs anywhere from $10-$20.
7) Splice the aftermarket head unit harness into the harness adapter you just bought.
8) The harness adapter will have 2 connectors. The black one is for speaker wiring. Plug that one into the black connector you found above the glovebox door. Plug the grey connector into the other grey connector directly behind the factory radio. Plug in your aftermarket connector to the back of the head unit. Don't forget to connect your antenna lead.
9) Reconnect the negative battery cable and turn the unit on to test and make sure you have power and sound. If all is well, button everything back up and enjoy your new stereo!

I didn't really need to remove the glove box door, as my black connector was right there behind the stereo itself. At first I was looking behind the glove box like in the write up, but after not finding it, I saw it right there behind the stereo wiring. Leave your factory amp in the trunk disconnected.

That is awesome, thank you so much!