Got everything installed this weekend and, man, what a difference! I didn't realize just how shot and saggy everything was.
Just to recap, I ended up installing four (4) new OEM Toyota Tokico shocks (purchased locally from the dealer) and Old Man Emu 2860 springs in the rear. This replaced original rear springs (w/ 252K on them!) and Monroe Reflex shocks with at least 30K on them.
Overall, it was easier than I was expecting and fearing. The fronts were a piece of cake, and I did these Friday night. The Monroe shocks have a hex-shaped bung UNDER the mounting cushions, so it is super easy to put a wrench on the shocks to keep them from rotating. The only hiccup is the weird 15/16" top nut that the fronts use. I didn't have a 15/16" wrench, so I needed to use an adjustable crescent wrench, which was not ideal.
I tackled the rears on Saturday morning. I (mistakenly) assumed that rear retainer nuts were also 15/16", so I bought a 15/16" flex-head ratcheting wrench, in addition to a 22mm for the new shocks. Well, the rear Monroe's were 19mm!

Luckily, I head enough room to get a standard 19mm box wrench up there, although it was tight.
Second hiccup came when the P/S sway bar bolt broke. Luckily, I had a couple of spare 8.8 M10 bolts lying around, so that was an easy fix.
The biggest pain came when I realize that the old P/S shock was firmly seized on the bottom stud. I used a torch, beat the hell out of it with a brass drift, and nothing would make it budge. I finally decided to cut it at the weld with a sawzall, hoping I wouldn't rupture the reservoir. Well, I DID rupture the reservoir and ending up spraying myself with hydraulic fluid!

More cutting and forcing with extreme prejudice and I finally got that

off.
Wrestling the springs in was a little bit of a challenge, but not too hard. The D/S--between the longer spring length and the brake hoses being on that side--was considerably harder that the P/S. I'm glad I decided to do the D/S first. Then, getting the rear shocks bolted in was a snap. Regarding my question above, I put the retainer with the flange UNDER the frame, and the retainer with the large hole but no flange on TOP of the frame. This made the most sense once I got under there.
The new shocks raised my front end by almost an inch, and I got nearly 3 inches in the rear with the new shocks and springs! Again, I didn't realize how badly she was sagging. My wife comes out as I am taking it off the jackstands and says "are you going to be able to fit out the garage door?

Well, I did, with only about a half inch of headroom to spare!
Ride and handling is great! Much more controlled, no floatiness, and much more confident over bumps, especially at highway speeds. Thanks to all for the advice and technical input along the way!