I've not removed my flies yet but am considering Moto's. Don't think re-mapping will be necessary.
So you still smell of fuel with Motobox installed while running Akra map. Just goes to show you how rich that map is, ie, way too rich. You shouldn't be smelling of fuel if A/F is around the 13/14:1 ratio. Sounds like that Akra map is putting you somewhere around the 11/12:1 F/A ratio. Too rich!
I'd set up a dyno day and have the A/F checked out as is with Akra map. If my prediction is correct load the standard map and try again. Keep in mind that the A/F is going to jump around a bit due to the stock mapping and that is precisely what the PCIII is for, to flatten it out at 13:1 across the board so in theory, should run smoother. My experience is the bike runs smooth enough on the stock map wwithout lean hesitation, running hot or snatchiness. Works for me and a couple of buddie's bikes I've set up exactly the same. You even mentioned your bike ran great before the Akra map. I'd consider going back to it simply for fuel range if nothing else. And, if you ride in the hills as I do, a slight lean condition at sea level fattens up nicely with a little elevation.
John