I never even tried to use the stock radio (any stock radio for that matter!) to drive the system - but I know the LC7i will give you a very good chance for success.

If the JL 3.5"s will fit in the dash (they should - please baffle them properly into the dash openings) - I'd go with a true 6x9" midbass in the front doors - quite a few descent ones to look at. You will have substantially more cone area and superior extension compared to a 6.5" in the front doors (and you really don't want the doors to run as full-range with a tweeter if you are getting that portion of your soundstage from the 3.5" coax dash speakers).

I'd also nix the rear-hatch speakers IMNSHO (wasted money). TBH - the ONLY time my rear-door speakers are faded on is when someone is in the rear seats and really wants to hear the system. Otherwise the rear door speakers (and especially the rear-hatch speakers) only distract and confuse the real soundstage that propagates from the front...

This brings into question your crossover strategy and quantity of discrete amplifier channels. I'd consider a passive DIY crossover from the 6x9"s in the front doors (a simple inductor will do in a pinch) to the 3.5"s in the dash (a simple 12dB/Octave L/C circuit to help with power-handling) - and let those share amplifier channels accordingly (2 channels drive all 4 speakers up front). Use the extra 2 channels for the rear doors so you can fade them (mute them ) as needed. Otherwise - go active for the front (using all 4 primary channels on that amp), and look for a tiny 2-channel amp for the rear doors (the rear doors should really be where you skimp if needed IMO).

Having every driver location on its own amp channel is advantageous for a number of reasons (time-alignment possibilities and crossover tweak-ability) assuming you can splurge for the DSP to allow it. 6-8 Channel DSP's start to get a bit pricey - but not out of the realm of sanity IMO.

Subs are a little light for my tastes - but I'm known to be a bit over the top with my SPL/SQL requirements. I'm sure they will be a nice balanced match for your front stage...