I finally have all of the system in and working. I swapped the Pioneer amp with the blown channel with the JL Audio JD400/4. Not only did that fix the issue with the blown channel, but the JLA sounds MUCH better and has significantly more volume compared to the Pioneer even though the RMS rating between the 2 is similar. I also disabled the factory EQ with ForScan and disabled the fake engine noise. The system already sounds really clean, but I still have to do all of the tuning because right now it is a bit flat in the mid range and has some spikes especially on the high end, right now the EQ on the DSP are still flat for each of the 8 output channels. I have a calibrated mic and an RTA app for my iPad, now I just have to do a little more reading on how to set a parametric EQ and find a couple hours to spend tuning it.
Don't tell my wife, but I am already considering replacing the Polk Audio 6x9 in the front door with either JL Audio or JBL 6.5" or 6.75" mid bass drivers. I am kind of leaning towards the JBL since I already installed JBL tweeters in the A pillars. JBL has a component system that includes the same tweeters I already have. I wish they sold just the mid bass driver since I already have the tweeters and I don't need the passive crossover since I am running the tweeters active off the DSP and JLA amp. Oh well. Maybe I can find someone that needs a couple 6x9, tweeters or crossover and recover some of that cost. It has been a long time since I messed with car audio so I forgot how slippery a slope it really is.