Well, a huge thanks to all for your input. This is one more project I can mark off as complete.
I ended up sticking with the factory amplifier as the thought of trying to run 8 speakers off of an inbuilt headunit amp just scared me. Series impedance is just not something most solid state amplifiers find fun or pleasant to deal with. I used a PAC 4 channel unit to take my head unit down to line-level outputs and handled the fitment via the tried and true cut and solder method.
It turns out in the end that I was smart to do things the way I did. The Harman Kardon factory system is 60 ways of wonky.
The rear 6x9s are bridged mono from a "sub" channel of the amplifier (I found this out because I only had one connected; more on this to follow). The rear 4" mid-bass are connected in series with separate coaxial tweeters affixed to the 6x9s, driven off of separate rear channels on the amp. And then the fronts are series connected, driven off the front channel of the amp.
The 6x9 discovery was made because one of them had stopped working. As I was testing the head unit to make sure everything was in order, I noticed the remaining 6x9 still worked regardless of the balance setting. The further good news is that the 6x9 I had reckoned to be blown was actually just damaged. One of the flexible links to the cone/voice coil had come loose at the cone. I was able to solder it back to the thin wire going to the voice coil and get the speaker working again.
Frankly, I'm very pleased with how the system sounds. It definitely took some tuning to get it perfect, probably more than would have been necessary if I'd rewired everything but I have all of my speakers working and I'd be rather hard-pressed to remember a system I've assembled that sounded as clean; granted that this does not have massive amounts of low-end grunt but it has enough to suffice. A side-benefit is that I still have my line-outs free on my head unit to add stand-alone amplifiers for a sub bass installation should I desire it at some point.
Anyway, it was far from the easiest install I've ever done. The wiring colours on the Saab make no sense whatsoever. The diagram at "TheSaabSite" was critical to my success. But it works, the JVC matches the colour of the Saab lighting and I merely need to find a permanent solution to the gaping hole in the dash left by the CD player.