*UPDATE*
Here is an album of the work I have done so far (The 6x9 mount was just a very quick job to test out the speakers and clearances)
4runner speaker install - Album on Imgur
I installed the front passenger 3.5" and 6x9 to test them out and compare them to the OEM speakers. The highs and mids sound much better, but the lows don't hit as hard as the cheap factory speakers. Another thing is with regular setting the highs can be a little harsh with the 6x9 3-way AND the 3.5" in the dash since they both have tweeters. I think if I just install the 3.5 in the dash and leave the OEM door speakers I can have the low end I want and the 3.5 can clear up the highs for me. (like most do with just the 3.5" Kappa's)
So after being underwhelmed by my initial listening I decided to do some more research. I found a few things... The factory head unit is a 4 channel 4 ohm unit. The front speakers are wired in parallel for a 2 ohm load. I cant get solid info on the rear from the forums, I would guess they are wired in parallel as well.
I also did some reading on r/CarAV and found the following basic info... most people don't like 6x9s, the front sound stage is most important, and components are recommended for the front
These are my new options:
1. return the 6x9s and 6.5s, keep the dash 3.5s and the under seat sub, run the OEM door and rear speakers. It will sound decent and only cost $190
2. return all the Kicker speakers and get a decent set of components, run the OEM rear speakers. My only worry is that if I get decent components that the factory headunit (no factory amp) wont be able to give them enough power to really sound good. If I have to add anamp the price is really going to jump.
KICKER | 6x9" CS Components[7] these would easily fit and are only $140
Focal IS 690TOY 6"x9" component speaker system designed to fit select Toyotas at Crutchfield.com[8] I really dont want to spend this much if they are only going to be slightly better than OEM + 3.5s
3. Keep all the Kickers and install an amp. I already have a harness adapter I made for the sub inputs so all I would have to do is add the rear channel outputs for the amp and the returns for all the speakers. The drawback is this is slowly creeping up in price, would the benefits of the amp justify the price?
Both of these have high level inputs and can fit under my seat
$118
PRIME Amplifiers R300X4 - Prime 300 Watt 4-Channel Amplifier | Rockford Fosgate®[9]
$89
GM-A4604 - <b>NEW!</b> - 4-Channel Bridgeable Amplifier | Pioneer Electronics USA[10]