I need your advice on how to determine which of my brakes are causing vibration. I don't have a clear idea yet if my problem is in the front brakes, the back brakes, or both. Here is what I have done so far.
I have removed the front wheels and examined the front discs. The pads have a reasonably healthy 5mm of thickness on them still. The discs appear to have even pad deposition on the outer surface. I haven't removed the calipers and shields yet to inspect the inside surfaces. I have carefully measured the disc lateral run-out on the outer surface, finding the passenger side at 0.0005" and the driver's side at 0.001", or in other words, very good. I have removed the rear drums and had a look, but could see nothing amiss. The right rear drum was overheating so I adjusted the shoes inwards manually and left them that way for now.

I need a method for isolating the problem to front or back. My test drives have been inconclusive. My attempt to slow the car using only the handbrake resulted in no vibration, but the car didn't slow down much either while the handbrake feel is a bit vague. I am considering an experiment to pinch off the rear brake lines using clamps and doing a test drive with only the front brakes active, but it seems that this clamping idea may not be a good one as I may damage the lines. An other idea is to effectively disable the rear brakes by manually running their shoe adjusters all the way in so the shoes don't really contact the drum and then test driving.
Do any of these ideas make sense? Can you suggest a better way to isolate my vibration problem to the front or rear axle?

I'm by no means an expert... but I would focus on the vibration itself before clamping any lines.

Is the vibration mainly in the pedal itself? steering wheel? whole car?

Tie rods are a super common issue with these, and if they are worn, even if your brakes are functioning properly, you may only get vibration on braking.
Might be worth it to jack it up and check out.

Good suggestion, so I took the 4runner out on the road to see what I could learn. It was inconclusive, as I did not go all that far so need to find some more time in the next couple of days to give it another shot.

When I start feeling a pulse in my pedal when braking lightly I start doing some really hard braking for a little and it goes away.


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That is interesting, and consistent with those that talk about re-bedding your brakes to smooth out uneven pad deposits on the disks. I've been thinking of re-bedding my brakes too.

In the meantime, while I am loathe to fire the parts cannon at this issue, I think it is time for this old 4runner to get some new drums in the back, so those will be ordered shortly. They are very little work to install, so really just a small investment in time and a few bucks.