Ok so I've been searching for the past two days on how to get my rotors off of a '98 SR5 Runner. I have the calipers ziptied up and out of the way and I'm trying to get the rotors off so I can have them turned. My impression from what I've seen is that they just come right off. I am not the smartest kid on the block but it seems like this should be easy and it's kicking my butt. Please help a cherry out as I am knee deep in this project, and am considering just putting new pads on and calling it quits.

 

It's likely just rusted on. Take a deadblow hammer and hit the backside of the rotor (or place a short piece of 2"x4" on the back side of the rotor, and hit the 2"x4" with a mallet). A couple of good hits should get it off.

That being said, if you get them turned, they will then warp quicker, due to them being even thinner than stock. 3rd gen 4Runner rotors are notorious for warping, which is why many 3rd gen 4Runner owners upgrade to Tundra calipers and rotors. My thoughts on turning rotors, is that if they don't feel warped when you're braking now (and you can check for warpage using a dial indicator and magnetic base so you know for sure), then I just knock the glazing off with a fine sandpaper, clean the dust off with brake cleaner, and re-use the rotors as is. If they are warped, I replace them.

 

I've been at my 3rd gen's passenger side rotors since Jan and finally got it off today.
Tried tapping with a hammer on the rotor hat and in between the studs...no luck...even with repeated PB.
Tried banging the back side of the rotor with 2.5lb soft deadblow covered by a rag (for the rotor's protection)...ane repeated PB...nope.
Tried a vice on the caliper mounting bracket and the rotor edge (with a rag)...maybe a budge, but no progress.
Someone suggested on other forums to obtain similar bolts that would thread through the caliper mounting bracket and push the rotor off as you tighten...haven't tried that option, maybe that's a possibility.
Went out and bought a large puller...that seemed most promising, but the center screw punch started to distort the hub center. It's a risk what it might do to the studs if it pressed up against something placed in between. My imagination stopped there.
So I went back to basics. Use more force on the deadblow when hitting the back side. I didn't want to mess up the rotor/pad surface, which was affecting how much force I was actually putting in before so I used a bunched up rag and this time put all of my one-armed swing...another...and another...and why not another because I'm starting not to care anymore about messing it up...BA BAM! Knocked it loose at last! It's been 2 months and I finally succeeded.

Good luck

 

Don't use the caliper holes and bolts to force it off. It won't come off squarely and you don't want to damage or bend the caliper mounting surface.
If everything is out of the way, (hub, 2 big nuts, a washer)? Is the outer bearing out of the way?
If so, get down on your butt and grab the rotor with both hands on opposite sides. Use a push/pull motion and try doing this on top&bottom then left&right. Watch your fingers and don't rotate the rotor with your fingers gripping it on the backside or you might be swearing some more before you finish.
It should start to move a little then more as the bearing starts to come free from the inner race.

 

That's not how 3rd gen rotors are set up. They are not bolted to the hub like on earlier 4Runners. They are simply free floating rotors that slip on over the hub and are held in place by the wheel being bolted on. Sometimes they get seized on the hub due to rust.

 

Okay my bad. That info I gave was useless in this application.
Now that I know that you have hats or slip on rotors here is my best advice; Never hit the back of the rotor with a hammer unless its a soft on or hitting a piece of wood. Do and you will NEED to turn them to get the rest of the pad surface as low as your dents.

First of all, with the truck supported, wheel off, and calipers hanging out of the way spray some WD or your favorite penetrant on all the stud bases (where you can see the separation between the stud and the rotor and also around the hub and rotor). A few good hits between studs to shock the rust apart and different positions of the rotor to let the penetrant seep in (spray some more after hitting.
Secondly if you see 2 holes in the rotor face that are threaded but just run into the flange behind it, these are used to force the rotor off without pushing or beating on the braking surface. A couple of 5/16 bolts (I know Toyota's are metric but trust me on this, I'm pretty sure). Screw 2 bolts into these holes and they will run into the flange behind and push the rotor off. Use even pressure on each bolt.. Don't just power one on do each one a little then the other. If it still wants to resist, remove the bolts and spray some more into the slight gap created by the bolts pushing on the flange. Some more hits with the hammer between the studs (only with the bolts removed) and she should submit to your APPLIED FORCE.
Another thing we used at our shop for rusted rotors or slip off drums was an air hammer with the wide/flat bit on the face of the hat. A couple rattles 180* from each other and she's putty in your hands.

 

toyota wasnt nice enough to drill the holes in the rotor for 2 12 mm bolts to run it off on the 96+ trucks and 4runners

 

Thats bunk.