The dyno on the website specifically states stock ECU, but as you said perhaps your truck being 4WD makes a decent difference. I believe the 4Runner has a different transmission from the Taco, too - if I'm not mistaken the Tacoma has a W59, but I think 4WD 4Runners (at least the V6) had the R151F. The drivetrain losses through the transfer case in the 4Runner could conceivably be a decent bit greater, too.
I considered switching to a standalone ECU as well, but the hassle of having to go back to stock for emissions isn't worth it to me. The power level that I'm at is fine with me, as I am more about reliability - the only thing that I take issue with is the ECU taking so darn long to switch from closed to open loop fuel control at WOT, but that's just something I live with. I don't know if you've discovered this, but if you roll into it instead of mashing the throttle, the ECU has a chance to switch to open loop control and timing does not get cut like it did during your dyno run...definitely is easier on the engine, and makes driving more fun since you're lengthening the drama of spooling the turbo. :lookout:
I do have a quick question: have you had any issues with your downpipe loosening on the turbo side? I have been having constant issues for the past year or so with the nuts coming loose on mine, causing a pretty large exhaust leak that makes the truck run like complete crap until I tighten the nuts back up. I've tried a couple different solutions, starting with new exhaust nuts and high-temp threadlocker (didn't have a whole lot of hope for that one, since that area's temp well exceeds the max for the threadlocker), and then when it happened again, I tried new nuts along with jam nuts, but they still managed to back off. My truck is actually parked right now since the issue has come up again and I just haven't had time to fix it for the past few weeks, but my next idea is trying deformed exhaust lock nuts and possibly new studs (all spec'd for high temp exhaust use, of course). If you or your brother has encountered this issue before and has an easier solution that I've overlooked, though, I'm all ears there. :shrug: