As a tech response, what I have to say seems a little bit aimless, but if anyone knows more about proportioning valves in the brake system, I'd be curious, even if it isn't applicable to the problem in this thread. ...
If you haven't found any of the vac/booster system at fault, consider whether the brakes ARE working at the rear wheels. Your description of the condition of the front disks, as you found them, might suggest that the disk brakes are doing all the work, and getting really hot as a result.
I've never done the drum brake test I am thinking about, but in theory you *could* sort of test the rears to verify that they're hauling the 'cruiser down when you stand on the pedal: Inspect the pads and drums for signs of pad wear, and while yer in there use some chalk or pencil graphite or prussian blue on the inside of the drums. Then go fo4r a drive. Then re-inspect the drums to see how the indicator you left in there has fared--all rubbed off by brake pads?
I'm asking this obvious question because in the back of my mind, I remember over-hearing something about the supposedly right way to bleed a brake system that has a proportioning valve in it. I've never given any special consideration to the proportioning valve, and I'm reasonably successful at brake work, so maybe what I overheard was nothing more than some idle engineer's theory or fantasy (or my own brain fart). In other words, unless someone with FJ60 brake expertise confirms it, take it with a grain of salt and don't worry about it, OK? Here's what I think I heard:
If you don't take this valve into account when bleeding at all four wheels (even one at a time), I think the problem was that you'd end up not replacing the fluid in one branch off the proportioning valve (whether that means you end up with air in the lines after bleeding, or simply will get left with old water-saturated fluid to corrode the lines, I can't say, sorry, but I suspect it is the former--air left in the brake lines). Anyway, I got the impression that it is dangerous not to take the valve into consideration in some circumstances, like when bleeding brakes while parked on an incline.
The disclaimer: it was a few years back that I heard this (memory of it is cloudy) AND I wasn't really paying attention because I have a tendency to dismiss and ignore safety advice when it goes against my work habits. I'm throwing this out to you just in case it means anything to your braking problem. I am not an expert, so take it with a grain of a salt.
That said, I will go try and pick up the trail again with the guy I heard it from. If I get more clarity about this business, I'll post the substantive stuff here in the next couple of days.
BTW, I went for months without having functioning rear brakes on my FJ60. Ya sure, ya betcha that stopping was hard, and dicey too--it pulled to one side pretty hard after a while. When I finally got all four brakes working again, it was a revelation just how good the brakes are when they work right. There are parts of the system that give me doubts--I am not a true believer in the "self-adjusting brakes" mechanism, because mine only seem to go looser, never tighter--but the brakes in an FJ60 are designed well enough, when they're working.
Good luck, and sorry if I've muddied the water .
--Ned