It just doesn't seem worth it to me to pay $567 for the fuse block.
Got my 4R'99 Limited with same problem -- cant lock doors with button on keys or driver's door. But fix it with ugly hack and ~$7
Problem: central lock cant lock or unlock doors. If you press lock/unlock button you can hear faint click somewhere near drivers left knee instead of loud clang of door locks.
Cause: dead relay inside "body control unit".
Solution: get new one and change it
Required skills: general with screwdrivers and good with soldering iron.
1. First of all find BCU. This is a big white box with fuses and a couple of relays behind the small door left to the driver's knee. Remove 4 bolts and plastic cover under steering wheel.
2. This box has a dozen or so cables plugged in to the back side so its not so easy to take it off. But you do not need to

Unplug "front" cable (mine BCU has two of them while in manuals I can see only one) located just under fuses. On my BCU it was additionally fixed with plastic clamp. May be it is better to disconnect main battery "-" but I ignore this and everything is still alive
3. Look closer to that white flat surface with cable socket(s). It is a cover with 4 clamps, two on top side and two on bottom. Take a thin "-" screwdriver, insert it to that square holes and push clamps towards insides of the thing. I broke one clamp

but managed to open the cover.
3. Under the cover you can find a PCB with some chips, relays and other electronic stuff. There are 4+1 relays. The biggest one is for door locks and is the source of our trouble (I hope). On this step you can plug the cable from "step 2" back to its place and try to lock/unlock doors while put you finger on big relay. You can feel relay shudder when you press the button and you can check that you find correct relay.
4. Disconnect main battery. And take PCB off its place. It is hold with 4 plastic clamps at corners and line of 15 or so big pins/sockets. Unclamp the clamps and pull off PCB from pins.
5. Relay name is "TAIKO
TB2-100" which is a pair of relays in H-Bridge mode. Get a new one if you can. May be Farnell or Digikey or other seller can deliver it to you. But here in Russia it takes at least 2 months to get it (if you are lucky).
So you can just get a couple of general type "5 pins 30A@12V car relay" with sockets and wires. Smthng like this:
6. Hard step is coming: desoldering relay. It has 8 pins, 4 of them rather big so you need a powerful soldering-iron, solder-sucker and other tools. In my case desoldering process ended with big nippers and relay totally crushed into a small pieces
7. Solder new TB2-100 relay if you have one. Or solder wires from two cheap relay sockets. That requires some skills and art because you need to put a pair of thick wires into a thin hole in PCB. The schematics is quite simple so I have no files or drawings, but if someone need it I can make it. Plug relays, install PCB back into BCU, plug cables and test it! Should work like a charm
8. Route wires to the side of BCU and cut a hole in plastic cover for it. Assemble everything in reverse order. Write a letter to Toyota and suggest them to use relays in sockets instead of soldered
This is not a 4runner problem. You can find same troubles discussed in other Toyota cars forums.