I would install a sub exactly where I did in the picture I posted. It doesn't block storage or inhibit any normal use of anything.
But maybe you're just looking for something like this install by Antman?
http://www.toyota-4runner.org/5th-gen-t4rs/92013-antmans-thread-24.html#post989173
For front door speakers I would install a pair of quality 6.5" or even 8" round speakers. Check out Dynaudio, Morel, HAT, Hertz for some good options. There are a million other great options - including good cheaper options but you haven't posted a budget.
For the upper dash I would install a 3" wideband speaker. Some people might say it's crazy especially considering their off axis but it sounds incredible to me. I know one user managed to get a morel hybrid ovation 4" point source speaker to fit but that would take some effort.
Rear doors use whatever you want if you want rear fill.
I'd leave the hatch speakers disconnected.
I would add a sound processor and continue to use the factory HU but of course that's personal preference and makes things more complicated. There are a load of good DSPs out there from Alpine to Audison and a lot in between.
For reference here is the link of the speakers I used in the dash and doors. L3SE in the dash and L8SE in the front doors.
HAT Speakers
If you wanted to try something like the 4" morel point source speakers in the dash and build a quasi 3-way system here are the speakers you would be looking at:
Morel Integra 402
The doors will take up to an 8" round speaker depending on the depth but you will need adapters/spacers regardless. If you don't want to make your own you can contact user Mr Marv on tacoma world, he makes quality spacers/adapters for reasonable prices.
Like I said there are probably 100 options that could be argued to be as good as the next so it will depend on budget, personal preference, etc etc.
I replaced all the speakers in the truck except the rear hatch a couple of months ago, it was a fairly painless process.