The MS-8 will help with tonality but it won't cope well with your mids and tweeters on the A-pillars. The reflections off the windows and dash will be measured as if they're several different speaker locations. It would be a lot easier to tune with any kind of microphone based measurements if you cut it back to as few speakers as you need. Have you listened to it with just the 3-way set?
Pioneer_AVH-4100NEX, Massive Audio Core-1, Cerwin Vega V600.4, CV V1500.1D, CV Stroker ST65C, CV V465 rear fill, CV VPRO124D 2.0 cu ft @ 36 Hz