Hmmm, I retrofitted the electric locker into my 99 4Runner SR5 4wd and as I recall, it was PARTIALLY prewired if you could even call it that. Oh yeah, that connector behind the dash doesn't connect to the RR Diff Lock switch nor is it related to the locker mechanism.
You seem to be on the right track though. I used the Factory Locker ECU from a TRD Tacoma (same exact part as in the 4Runner) and took advantage of some of the stock features (only engaging locker below 5mph to prevent damage to the locker ****clarification: must be below 5mph to engage locker, but once engaged locker will continue to be locked at any speed****, potential ability to disable ABS with locker activation--need a different ABS ECU for this though) and improved upon them (allow locker to function in 2Hi, 4Hi, and 4Lo as opposed to the factory "4Lo only"). Also was able to add a wire to the back of the combination meter to take advantage of the FACTORY "RR DIFF LOCK" dash light--yes, the light is already there just waiting to be lit up for the first time.
Lots of connectors/wiring harnesses are just slightly different on the factory locker equipped 4Runner. However, good use of a multimeter, splices/soldering ability, and some extra wire (a good length of 5-wire insulated trailer cable as well as some single lengths) will let you take advantage of much of the stock wiring and leave you with a completely factory appearing system. The factory manuals and wiring diagram help a whole lot in figuring everything out.
I had a local shop do the the grinding work to my rear axle to let the locker 3rd member fit. And I did all the wiring myelf--really not too bad at all once you understand the role of each component and where to find the important connectors and wires. You'll have to get a little creative if you want to take advantage of the factory diff lock dash light and RR Diff Lock switch since you'll be running individual wires to key pins on existing wiring harnesses (but it is totally worth it).
Tips: 1)run the trailer cable from the locker ECU to the rear diff out of the cabin where the left rear passenger sits (look under the carpet). 2) buy the wiring harness that attaches to the rear diff locker actuator (you can splice your trailer cable wires to the other end of it, and then seal/waterproof them) and the end that connects to the diff itself will snap right up. 3) Extend the diff lock actuator breather while you're doing the install (this is really the only weak point of the electric locker that I can think of--the factory location only puts it a foot above the rear axle or so--and more than 1 electric locker actuator has rusted out by getting mud/water down that tube.)
I have posted this info (and a whole lot more with pin assignments and other stuff), but it has probably been deleted--and its slowly finding its way out of my memory too. I've had the locker in for about 2 years now and it is totally awesome--no complaints at all. When you actually have the 3rd member in front of you, you'll see exactly why the locker sleeve splines need to lined up for the locker to engage--some people think their locker is taking too long to engage or disengage but it is really just dependent on the splines being lined up--crawling forward with the steering wheel turned will let the splines line up for engagement. And if having a problem disengaging just give a little gas and then let off to unload any pressure from the splines. I think it would be pretty easy to adapt the e-locker to a 2wd 4Runner--heck, the 2wd Tacoma TRD Prerunners have them, why not a locked 2wd 4Runner?

Then again, I guess you could always get the Downey cable activated switch for the electric locker??