Hey folks, just wanted to throw my experience in here. I purchased a 2015 FJ-09 with 1600 miles on it last year and could never get comfortable with the throttle. I read everything here and got sidetracked with a home purchase. Having forgotten about the APS modification I sent the ECU out to Vcyclenut for a flash last month and I was quite disappointed when the flash didn't improve the bike much over stock as far as throttle response and found riding in B mode to be much more in tune with how I like to ride and actually enjoyed the bike. I finally remembered this thread and followed the instructions. In the end I dialed back diag 14 to position 13, and diag 15 to 12. For me this change is what I was hoping to achieve with the flash. I'm not at all sorry for having the flash done, however, the APS change has transformed the bike from B mode being the only enjoyable throttle to STD mode now being what I hoped it always would be. It's still a little aggressive going from off-throttle to on-throttle at high RPM (7k+) and I may dial it back to 12, possibly 11, to see if that clears it up.
All that said, my advice to anyone reading through this thread looking to smooth out the throttle, doing this mod is where you might wanna start before spending any money.