Thanks VP, that's good stuff!
I did find this quote in the PDF you uploaded:
It doesn't EQ phase separately from frequency magnitude, but in my experience, that isn't necessary so long as
you have a center channel and a matrix or some other center signal extraction method or time alignment. MS-8 has both.
This makes it sound like the MS-8 isn't actually making phase-centric corrections, but they haven't had a reason to. Your quote about time alignment above 3k is extremely relevant as well, since that's where most component sets are going to be crossing over in these cars.
I've been trying to develop my plan so I can start "phase 1" and here's what I'm thinking at the moment:
Front - Rainbow SLC 210.25 NG
Underseat - Stock HiFi
Rear - Stock HiFi
Sub - JL Audio 10" W6v2
JL Audio XD600/6 (Front, Rear, Underseat)
MTX class D (Sub - I have it handy from my last car)
JBL MS-8 (Of course!!)
I'm a little nervous about running the OEM speakers off an aftermarket amp, but I read somewhere that the stock HiFi amp has some terrible distortion and I'm also not sure how well it would like being on the receiving end of the MS-8.
In this case phase 1 would be the front speakers and the JL amp, probably leaving OEM speakers on OEM amp for now.