im reading all your threads and trying to help yah. i like your plan and i think you still know as much as you did befor.... lol
your plan is cool if your trying to do a budget build. get a 4ch amp and try to get one that fits under the seat for a clean install. if you bought the 6x9 already you need the adapter plate or get some wood. the adapter plates are cheap on ebay and the rears need them too. Look for taco ones if the 4runner ones are not listed. look for some 6.5 3ways that match your 6x9's and just run them to the 4ch amp.
As far as the wiring get alot of speaker wire so you dont have to hack up the stock harness. splice in a line out conveter for the rca's behind the head unit and wire the door speakers directly to the amp. I would run the stock tweeters from the head unit cuz they dont like amps very much. this and the amp power wires and your done.
the sound of 4runner wont compare to a is300 it doesnt have a rear deck. the rear speakers on the 4r are so low your gonna be hit or miss with the rear sounding good. But, your gonna have your rear passengers not hearing much. So, thats why i say get the 4ch. if your budget is for the a 2ch then just amp the front 6x9s.
if you wanna just do it in steps just get some 6x9s and the adapters in the front and build up from there. you can always add an amp later, this would be the best bang for the buck. haha