OK, as an owner of a 8,000 pound (when fully fully loaded for long camp trip with no resupply) tacoma that can lock up the tires on pavement, I can provide some insight from my trials and tribulations with a heavy taco. And I won't debate or argue with anyone on what I should have done, why it is so heavy, whether I should have a different truck, etc. It is what it is.
A few things that I didn't see yet - do you have a vacuum booster or the electronic booster found on TRDOR and some other models? That makes a difference. Huge difference in your options.
I have TRD sport. Vacuum booster. I started small, pad upgrade back when I was in the 6500lb fully loaded range. Sucked, downright scary in a panic stop. I tried a few sets of pads and rotors, no real difference. Although, I can tell you with confidence, the best pads I've run are the EBC orange extra duty. They are specific for heavy trucks, 4wd, larger tires, etc. With the sport rotors they made a big difference, but I never ran those in stock size (read below). I have never tried, nor will I ever pay, for the BBK stuff that is out there... way too expensive and not easy for consumable parts, etc. Truck continued to get heavier and heavier with upgrades and gear, suspension and reinforcements for the weight, cause more weight, etc... On the heaviest outing I've ever done, family of 4 for 5 days to the beach with no resupply, bringing firewood, water for showers, etc... it weighed 8300. Not kidding, on a scale. So that is some background.
The real upgrade you should look at, IMO (which you will need larger 17" wheels for):
get a late 5th gen 4 runner brake upgrade. I bought new calipers, and the EBC sport rotors and extra duty (the most aggressive pad for heavy vehicle, non race) pads for the 5th gen 4 runner. Bolted right up with trimming to the backing plate (or buy 4 runner backing plates). They have larger pistons in the calipers for more hydraulic force applied. This is a big difference but will make your brakes more soft, not only cause the larger diameter of the new caliper pistons relative to master piston size, but the EBC orange pads are a soft feeling pad as well, they bite really hard at the same time they don't feel very firm on the pedal. The TRUE best thing you can do to the brakes though, is get the dual diaphragm booster from a sequoia or tundra, and put that in. It will double the boost of the power boosted brakes compared to the crappy single of the taco. To do this, you need to get the master cylinder out of the same vehicle since the bolt pattern on the master and the booster are different. I picked up the pair at an auto recycling place. It will bolt in with mods to the pushrod and some adapters and brake line mods. There are threads on this. Getting it bled properly can be tough. When you get the tundra master, it has a larger piston. then it is assisted with a dual diaphragm booster. and pushes onto larger pistons in the calipers. Compared to stock, this will put your head passengers into the seat belt when good pads and rotors are used.
If you choose to not upgrade the wheels and therefore not get the 4runner brakes, I would still do the tundra master/booster swap. If you have a TRD offroad, I would still do the 4 runner brake upgrade, it will work with the electronic booster still. But if you are firm on staying with 16" wheels, that will be your Achilles heel. The early tundra brake upgrade that does fit in 16" wheels is nowhere NEAR as good as the 5th gen 4 runner upgrade that won't fit in the 16" wheel.
I have also gone above and beyond with the rear brakes, when people told me they couldn't be improved. Bull. I understand rears do less work than fronts, no question that upgrading something that only does 30% of the braking will not have as large of an effect as the fronts... but when you are heavier, and the weight is on the rear, I feel the rears should be upgraded too, especially when you have done front upgrades making the imbalance worse. I put larger wheel cylinders in the back, and experimented with a few different types of pads. My testing isn't complete yet, and I haven't fully documented it. But I can tell you that a wheel cylinder size increase in the back does help for a truck like ours with lots of rear weight. When I get the brakes up to temp (sometimes I drag the ebrake a bit for 1/2 mile in cold weather), I have absolutely no problem howling all 4 35x12.5 r17 mud tires on a hard stop, and it is very controllable, very low pedal pressure.
(edit: these brake upgrades make the Tacoma brakes absolutely fantastic. The wrong year of Tundra master cylinder and booster was previously posted by...
www.tacomaworld.com
Looking for rear brake upgrade advice. I'm not interested in a disc swap at this point, so please don't go there. Truck is VERY heavy expedition...
www.tacomaworld.com
If you want to talk more details, PM and we can exchange phone numbers. That would take way less time than what I just put into writing this.