I have my radiator drained already to deal with temp sensors and a lower radiator hose, decided to try and take care of this as well. no heat coming from the rear heater in my 1990 4runner. The fan works strong at all ranges,so I figured I would just remove the hoses and flush it out. I can also replace core and temp valve with a spare i have in my parts pile.
My questions are :
1. are there any spots that indicate some sort of failure.
2. how do I burp the rear heater system after fluid change.
3. best place to drain from.

 

Did you get this yet?
I can't answer number 1, but to burp the system you'll need to have the front of the truck as high as possible.
I haven't yet put mine back together, but you made me think of some issues. The way that rear core sits higher than those two feed (ok, supply and return) tubes, seems like a great place for a bubble.
Now, I buggered up the soft round pipes on the exchanger itself, but my eventual plan is to pull both return/supply hoses off at the firewall, and sort of plug one and use a hose to fill and push out as much air as I can. That won't be RO water of course, so I have to think on that. Sort of like bubbles get pushed to far point on any hydraulic system. Not worried that it will be all water, because eventually it should mix with the coolant, no? Just not thinking tap water will be good.

On 3, not sure there is a good place to drain. I took engine out like 2012?! And in '16 when I got around to working on it again (for a brief spell, mind you), there was still coolant in the rear core.

 

Yes, I took the lines off after draining the coolant system down to do a knock sensor. the hard lines that travel down the frame rail under the vehicle became clogged with coolant stop leak flakes. I've put 100 psi into the tube with my blow gun and cleared the return line out, but not the supply to the rear core. I've been running wd40 through the hard line to soften and hopefully break up some of the corroded junk in the tube. It appears to be clearing up little by little and letting some of the air through to my catch bottle.