SOMETIMES, although a very rare occasion, some drive-by-wire settings must be changed in the tune for the 4.10's. My car happened to be one of those rare occasions. This just goes to show how all cars are different, and not all ecu's function EXACTLY the same. You MOST LIKELY won't have to worry about this problem, but nonetheless here is a heads-up that this complication IS out there just in case it happens to you.
Apparently, the Spanish Oak & the drive by wire system closely matches rpms vs. vehicle speed... it seems some ecu's more aggresively than others. When I installed my 4.10's, I flashed my tune to fix the speedo. Quite often I would then get "the wrench of death" when I went to WOT at certain speeds. Evidently, the drive by wire system was seeing that my rpm's no longer matched OEM vehicle speed. If I reflashed my ecu back to having stock gears, I no longer got "the wrench of death." In reality, my speedo was now off; but as far as the ecu was concerned, my rpm's were now matching vehicle speed.
My solution was to get a new tune that would not only change the speedo for 4.10's, but also changed some drive by wire settings for the 4.10's as well. After I got my updated tune, all is well. Evidently, my ecu compares rpm/speed/load very aggressively.
I'm guessing you could kind of change the car's tune for the pully swap. You can change the rpm your car idles at for instance. Would that be of any benefit at all?