Do yourself a favor and get some Tacotunes mounts for 6x9's and the tweeter mounts or 6-1/2 normal speakers. Replace both of those with some aftermarkets. I picked out Pioneer tweeters and Kicker 6x9's (You will have to hardwire at least the tweeters) for $130 total. I did end up powering my 6x9's with an amp but you don't have to. The stock speakers actually don't sound tooooo bad but they're fabric junk with foams surrounds and a magnet the size of a dime.
As for headunit I highly recommend getting an aftermarket one even if it's a $100 JVC or Pioneer especially if you're adding a subwoofer. The stock stereo does not allow proper tuning for an upgrading system not to mention the headache you're going to go through trying to hook up remote wires, rca's and filters.
Wiring Kit: Preferably 4 gauge - $75
Spool of Wire: $20
6x9 speakers: $100
Headunit: $150 (Just to play it safe)
Sub: $100 (Build your own box out of mdf and you'll save yourself atleast 100 bucks)
Amp for sub: $200
Amp for door speakers: $150
Tacotunes mounts: Cant remember how much they are but lets say 60 bucks.
So basically your talkin about 900 bucks for a full system including headunit, amplified door speakers, and sub which should give you some badass sound if you buy good brands.
I agree with everyone crutchfield is the way to go for most stuff because they give you free brackets, stereo connectors and installation instructions. Do note that they don't make brackets for 6x9 speakers which is the stock size in your taco. Also definitely don't get the metra headunit bracket, get the scosche, you will have an option at checkout. The metra is crap and the scosche fits awesome to put it simple.
Don't forget if you want awesome sound, the tacomas also come with speakers in the ceiling! Replace those and you get great highs right on top of your head.