Well, sorry about that. I guess if anybody else needs to know how to do it then they can read my ramble. Lol.
Here is a thread you should check out. These guys are cutting a splicing, which I know you don't wanna do. But! It looks as though they figured out exactly what wires belong to what.
How To: Aftermarket radio wiring with stock SVT sub and amp.
I have never seen a factory sub/amp so I don't know if there are any inputs on them. Specifically RCA in. If your head unit has preamp out then you could run that RCA to the trunk. I know it's not ideal but that would avoid your hacking up the factory wiring.