The HO alternator is going to provide extra current, not storage. Using a large AGM under the hood and Li-on in the rear would be the place to start. Something like this:
Amazon product ASIN B08LQ27L6Y
Has all the distribution connections you;ll need, awesome addition to any high powered system. You might not even need an upgrade to the Alt, with a good Li-oN setup in the rear. As for speakers, bail the rear deck as having powerful subs in the trunk means you have to isolate the rear deck speakers and there's no real benefit if you are using the rear doors for fill anyway. I would consider an 6 channel DSP amp like the Helix, Sony or AudioControl units for amplification.
Something like this:
Class-D Full Range 2-Ohm Stable 6-Channel Amplifier. 3-way protection circuitry (thermal, overload, and speaker short protection). Variable low-pass filter: 500 - 5,000 Hz. Variable high-pass filter: 30 - 300 Hz.
125x6, drive front 6.5's and tweeters with 4 channels, a pair of coaxials on passive in the rear doors then the sub out to your HCCA bass amplifiers.
If you want volume and SQ, check out the Stevens line of midbass and coaxials to foot the bill, For the money the SB acoustics are really, really good.
These up front in the doors:
SB Acoustics SB17NRX2C35-4 6" Woofer, paper cone, new version, 4 ohm
www.madisoundspeakerstore.com
in the upper door or A pillars:
SB Acoustics SB14ST-C000-4 1" Tweeter w/grille- 4 ohm
www.madisoundspeakerstore.com
For the rear:
https://www.madisoundspeakerstore.c...cr25-4-coax-6-paper-cone-coaxial-4-ohm-round/
The tweeter leads are exposed and you should run a 12db Butterworth alignment xover at 2600 hz. Here are the values for that inline crossover to the tweeter:
C1 = 10.82 uF
L1 = 0.35 mH
Skip the 12db on the 6.5 as you'll run them off a HP filter from the amplifiers DSP and the fronts will be fully active DSP. the rears can roll off naturally or you can use a .24 coil (6db slope), all of these are pretty small and easily acquired. I have all of these parts laying around should you go that route, I'm unloading inventory at postage plus the cost of a latte!