This is how my 2011TE449 was from new too, there seemed to be a noticable hole in the maps just off idle. The things that cured mine was raising the TPS idle voltage (to richen the mixtures) & increaseing the idle speed to the correct speed.
I think I have tried just about everything except adjust the idle so im going to do that next. I'll turn it up a bit and hopefully it adds enough fuel at those revs to iron it out. Then I can reset TPS again, and adjust tuner. It is a lot better than when it had just Map 2 and the 2011 maps so I am happy but its just so close to perfect I really want to iron out all the problems and then have the perfect bike all winter. I will let you know how I go, BTW thanks for everyones help, I would've been rooted without you's!!
You could try adjusting the tps, pushing you further into the oem mapping. But the real fix for this issue is the pc5. With the pc5 you can add as much fuel as needed, plus you can set your accelerator pump from 0-2% throttle opening to give additional fuel only during that time and not during any other throttle openings. You can also set your tps position electronically with the pcv or make necessary voltage adjustments to your hardware just as easily.