The wiring was finished Tuesday night. In actuality I removed the rear blown amp, as well as the wire plugs that go into it. With a diagram I had that details what each wire is I removed the wires from the plugs and connected the speakers in parallel for now. Yes, the Sony head unit goes into auto-protect mode if I turn it up too much. However I don't normally listen at that high volume so I'm good for now. There is no distortion at all and the Sony radio's internal amp sounds loud and very clear. I should have by-passed the JBL amp from the beginning. Once the snow starts to fly the Mark will be put to bed with a cover in the garage and it won't matter at that point since I won't be driving it to listen to the radio.
In the spring I'll directly re-wire the speakers correctly with Monster Cable from the radio, bypassing the vehicle's speaker wires. The tweeters will be wired in parallel with the Infinity Kappa 6x8s that I installed at their corresponding locations in the doors and rears. In other words, all 8 speakers won't be parallel as it is now, just each individual 6x8 with their tweeter.
Rod - if you're still here I can confirm that the Scosche wiring matches the Sony radio wiring color-for-color. See the images below. I removed the Scosche converter since I didn't need it anymore and directly connected the wires that went to the green Scosche adapter going to the factory wiring.