First off... A BIG and long overdue THANKS! to BigFishAllDay for the great write up on the 3rd Gen 4Runner w/Tundra Brakes upgrade. That was very well done man!
I say long overdue because I did my upgrade June 2011. My upgrade included:
2006 Tundra reman. 13WL calipers from DiscountBrakes.com
OEM 2006 Tundra pads
OEM 2006 Tundra shim kit

Installation was about as easy as BigFishAllDay made it look. Overall I like the upgrade and the brakes feel very powerful, but i don't like the pedal feel. A typical brake application feels spongy and pedal travel is longer than before. My wife even noticed recently and asked me if they were safe. I’ve read posts where others have the same symptoms. Over the course of a year, I've pumped at least 4 quarts of fluid through the front calipers in an attempt to purge any hint of air, still spongy. Thinking maybe something in the rear was at fault, I rebuilt the rear wheel cylinders with new OEM pistons. Installed new OEM shoes, checked parking brake adjustment (it was perfect and needed no adjustment), then ran about a quart and a half of fluid through the rear... and still no noticeable change in braking whatsoever. I found posts where some 4thGen owners had a new shim kit installed to address spongy/inconsistent pedal feel, so I temporarily removed my front shims... no difference, so they are back in.

I read some comments in the thread about the increased caliper fluid volume being the cause and it seemed plausible, so I did some digging. Everything I find says the cylinder bore on the tundra caliper is 45.5mm. The 4Runner has two different specs, 43MM for non-16” wheel equipped, and 45.5 for 16” wheel equipped. So thinking about the amount of fluid that moves from the MC to the calipers, it seems like piston bore and piston travel are the only contributing measures, internal volume of the caliper really isn’t relevant because once it's filled, it's filled. The only fluid volume displaced from MC to caliper is the amount needed to move the 8 pistons in their bores. Knowing the 13WL pistons are the same diameter as my original pistons, the only variable now is the distance the piston travels out of the bore, or really how much it returns into the bore after a brake application. Corrections to my info or theory are definitely welcomed.

What is very consistent is that a quick little primer-pump followed by an immediate and real brake application results in what I would say is perfect pedal feel and travel. That second real press of the pedal feels exactly right, nice and firm, even with a little feedback, and the travel is much shorter, like I remember it. I know this sounds like air in the system, but I just don’t see how it’s possible. During all of that flushing, literally a gallon and a half, and the reservoir never came close to empty.

Has anyone considered the Toyota SST that actuates certain components of the ABS/VSC brake pump system and if that little activity is a real necessity when bleeding/flushing our brake systems. I’d love to hear some thoughts or suggestions.

I've heard of the ABS system requiring a special tool to cycle the ABS to make sure the air gets out of there when bleeding, but I have no personal experience with it. Sounds like you've bled the system more than enough at this point, I'd suggest you have very little to lose and much to gain by trying it out.

I didn't get a chance to do this upgrade to the Surf, but this was always an issue I feared from reading others experiences, there's lots of people that would benefit from you finding a solution. Good luck.

Someone else here mentioned going out to a dirt road, get up to about 15mph, and hit the brakes HARD and don't let off until you are stopped. This will engage the ABS and should purge any air from that system. Then just drive home, bleed the brakes again, and you should be good to go.

Or you could just drive down a road with a couple leaves, maybe some pine needles on it and get on the brakes, I guarantee the ABS will have a fit

Or around here all you have to do is drive down the street and a deer with run out in front of you.

That's a really good idea, and easier to DIY!

How do you know if you engaged the ABS?

I dont have any experience with this swap myself but i wonder if the master cylinders are swappable from the tundras or sequioa(i think this was a fix for them also for rotor warping) to the 3rd gens. The master cylinders in tundras and sequioas may push more fluid then ours. Ive read of people swapping masters also on similar brake upgrades.

Never had an emergency stop? Fortunate. You'll know when they're engaged. They pulsate violently and make a horrible grinding noise, both of which are normal. The intent is to replicate you manually pumping the brakes, only much much faster.

I've read of a few others having similar issues after the Tundra upgrade, but I never did with my 199mms. I just had a buddy bleed while I pumped, and all has been good for over a year.

Also, shout out to another Tennessean!

I know this post is 10 years old, but I am having the EXACT same issue. Do you remember what fixed it for you? Thanks!