As I've been researching more, it's looking I may need to be the guinea pig if I want this. I don't think there was a whole lot of interest before, since until recently the tacoma wasn't tunable from what I can tell. Plus, however the demographics divide, it seems the 4runner worlds just ends up less interested in tuning vs the tacoma owners.
I've been able to find an 05-06 tacoma wiring diagram as well as the ECU pinout, and the same for a 2006 4runner to compare. I'm still double checking the wiring diagram, but it seems that they should be plug and play. For some reason though, the tacoma ECU appears to hold the same part number between 2wd and 4wd, the 4runner has different part numbers, but pinouts seem the same. Outside of the ECU, some other circuits look different but so far have the same apparent function, they may just be drawn differently for the same thing. For how toyota likes lean manufacturing, it would be odd to have different circuits.
But that brings me back to the ECU, why would the Tacoma and 4runner have an ECU for the same function, that are different. When I've asked, the tuner companies have responded that toyota had a limited supply of each kind of ECU, and just happened to give the Tacoma the tunable type, while the 4runner got the luck of the draw. Maybe their main supplier could only supply so much, so the 4runner had an extra supplier for their line, to make up the slack. Maybe that extra supplier had different circuitry for the same control. It's really all hypothetical unless you could get someone from toyota manufacturing to talk... unlikely.
If the pinouts appear to match so well, I think I will go through with this. The next part will be if a tacoma ECU can be programmed for a 4runner VIN. The keys are supposed to be the same basic part. I need to look up how the programming of these works.
My goal isn't so much for power, if I need more power I can push the pedal further and have plenty for my needs. I would like better drivability, tuning the shift points a small bit (mainly the 4-5 upshift that happens too soon under low-moderate acceleration, killing the progress), getting rid of the annoying downshifting while coasting, and I may also try a lean cruise tune guided by cylinder temp, coolant temp, and egt.