Which stock stereo do you have ? I think there are at least 3 different ones that I know of in the new 4Runners.How much knowledge of car audio do you have?Who's going to do the "clean sweep"? A prof. car audio shop would be best,and they should know.
I hate to say it but the non nav stereos with their orange lights suck and are extremely hard to see if its sunny out. Toyota really dropped the ball there as they are not bright enough.Heck,I have NAV which I can see great,but I have a hard time seeing the orange lights for climate controls,fan,ect down below the NAV and the ones up above it when it's sunny out. I have to take off my sunglasses and still bend over and squint! Bad design,not bright enough!!Everybody call/e-mail and complain and maybe they will fix it.
Speakers ,except the one's in the dash should not be a problem to swap. You just have to know how to pull door panels and the side panels in the back off to get to them. I usually use Infinity "Reference" speakers as replacements as they are pretty good quality for the price .Boston Accoustics or JL Audio speakers if you have the big money!But speakers are only good as the amp/stereo driving them.
I had the ones out in the back hatch for the Party mode and they were JBL 6 1/2 coaxials. Not up to normal JBL quality but don't sound too bad.I highly doubt Party Mode would work with an aftermarket stereo as the switching is probably done in the stock stereo's amp.