Okay guys, sorry it took me so long to get back here...
I now have an awesome sounding system with the factory HU! I installed the following speakers:
Shelby Kicker 8" subs in front door (These are supposed to be 2ohms but I think they might actually be 4ohms)
Polk Audio MM571 5x7's in front doors and rear deck (These come with an external crossover you have to mount but there's plenty of room for it)
TC Sounds TC-1000 12" sub (dual 4ohm VC's)
My factory sub amp was under the dash, on the driver's side, mounted all the way to the left. We pulled the wiring harness plugs and tapped into them. We confirmed the input wires were indeed low inputs. We cut a set of RCA's and wired the RCA's to these low level factory inputs. We also ended up routing the speaker wires from the aftermarket amp back up to the wiring harness for the 8". The factory subs were DVC and the Shelby's are SVC, so we went ahead and used two strands of factory wires for each Shelby sub.
Early on we discovered the voltage from the low level inputs was too low. So I purchased an AudioControl Overdrive Plus Line Driver which amplifies the voltage. This got us more than enough signal. Next in line after the line driver is a Kicker KX2 2-Way Crossover which allowed me to send mid-bass to the 8" and the low bass to the 12". The RCA's from the Kicker go to 2 separate Eclipse ZA1200 amplifiers. One of these amps powers the 8" and one powers the 12".
A couple notes would be that the factory remote wire does not put out enough power (5V) to turn on all my components. I currently have an Add-A-Circuit wired to the under-hood fuse box. Soon I'll have a relay soldered in that will allow the components to work from that signal (12V).
Also the Polks are highly efficient 2.7ohm speakers. They actually sound pretty darn good with the factory head unit but a bass blocker of some sort is needed. I ordered some 200uF 100V Non-Polarized Capacitors from Parts-Express which should do the trick.
Also, I had some 4 gauge Raptor wire for my power and ground connections. That wire sucked and wouldn't have been enough even if it was true 4 gauge. I upgraded to KnuKonceptz least expensive 1/0 power and grounds, running to their distribution blocks, then 4 gauge out to the components. I was absolutely shocked how much better the system sounded, with the exact same gain levels & volume, as soon as I installed the KnuKonceptz wiring.
In the end my system sounds great and I'm not even blocking the bass to the 5x7's yet! It looks pretty much factory unless the look in the trunk or fold the seats down, which I like. I still have all my Sync functionality which was important to me.
Hopefully this info helps someone else who is thinking about tackling this job!