The two most common causes of brake pulsation are rotor run-out (WARPAGE) and/or thickness variation (Out of parallel). Your 4-runner has fixed caliper design which is much more sensitive to runnout and parallelism issues than most other cars that use floating caliper types.
As a result the specifications for runout on the 4-runner is .001". Cars with floating calipers are usually .003". This can be measured with with a dial indicator. You can pick one up at Harbor Freight pretty cheap ($20-$25).
As far as machining your rotors on a bench lathe (off the car) I do not recommend it. The reason is there are many variables introduced by the bench lathe. Such as the lathe adapters, the condition of the rotor mounting surface called the "Hat." Also a consideration is the hub surface. Any rust on the hub surface will hold the rotor away from the hub in that area causing run-out. Keep in mind this can also be an issue even when installing new rotors. You want to use a dremmel on the hub so it is as clean as possible before reinstalling the rotor.
I have done the research on this and can tell you that a bench cut rotor will have .003" - .006" of run-out after being reinstalled on the car. One caveat, in areas with low rust (the Southwest/Texas) there is not as much rust and you are more likely to get away with a bench cut. But I cannot overeremphasize the importance of measuring run-out after the rotor is re-installed to make sure it is within spec. Now if you do decide to do it this way, and your measured run-out is out of spec. you should try and phase match the rotor. What this is is simply rotating the rotor one position on the hub/studs then remeasuring with your dial indicator until you find the position with the lowest measurment.
The only proper way to machine a rotor on any car, but especially the 4-runner is to use an On-the-car brake lathe. This machine will cut the rotor exactly as it runs on the vehicle. It eliminates all the variables, and will eliminate runnout. A good OCL (on car lathe) will cut the rotor to less than .0005" run-out. I have used a bunch of them but think the Pro-Cut is the best. If you go to Pro-Cut.com they have a list of service centers that have this equipment. This is the machine approved by Toyota.
As far as other opinion on this thread about calipers causing the issue or pad residue, I flatly disagree. Everyone is entitled to thier opinion but that is patently false. If someone in one of my shops said that I would send them to the lube bay until they figured out what they were doing.
I hope this helps.