I just replaced all four rotors. new pads (all oem parts) all around and completely swapped out all of the old brake fluid. applying the brakes in sudden stopping situations requires a very heavy foot. even then stopping quickly is a bit scary. all calipers are working properly. what are the next itms to check. 2003 sr5 4wd 180k miles. thanks.we have two other 4runners a 2003 and a 2004.. brakes on those vehicles are much more responsive. Phil

Could be one of several things causing this or a combination of all of them, sticking calipers, brake booster electric motor/pump/accumulator issues and deteriorated rubber brake lines.

If the calipers are sticking slightly it can cause you to use more force to achieve proper braking.

If there an issue with the brake booster not building up pressure, holding proper pressure, etc. you will have to use more force in braking.

If the OEM rubber brake lines have deteriorated to the point that it has dislodged bits of rubber or swelling inside the line it can cause heavy footed braking issues as well.

I would start checking to make sure the calipers pistons are moving freely(you may have already done this when doing the brakes), then move to replacing the brake lines (if they're all original from 2003 I would replace no matter what else you find is wrong)
and if you still have the braking issue go to the brake booster.

There could definitely still be a bubble somewhere in the lines, not hard to do with these systems. If you have fresh hardware, everything is clean and moving surfaces are lubed, and if your calipers aren't sticking...tough to not blame something electric or mechanical, but then you did flush the lines, so I would double check that before condemning parts.

Stupid question, but were your rotors zinc coated or bare metal? If the latter, did you make sure to clean off the protective oily film?

If the brake pedal is very firm or difficult to depress, I would lean towards a brake booster issue. Soft/spongy would indicate a hydraulic issue/air in the lines.

I would say the brake booster is not giving enough pressure.