ok first you need to understand fuel injection and how the ecu works. suggest a degree in mechanical engineering and a masters specialising in fuel injection systems.!!!
Seriously though
firstly the jd tuner reads the signal to the injector, things like length of pulse, how many pulses per minute, . it then interprets these as to what it thinks the throttle is doing eg being whacked open quickly, turned slowly etc, what its position is, what rpm is.
it has several adjustable parameters which the end user (me or you) can change. it describes these as if they were for a carbed bike, this helps us understand whats going on as i doubt anyone would make a lot of sence of a 3 dimensional ecu fueling map!
green and blue lights are idle so how the carb would act on tickover
green is 1/16-1/8 throttle etc etc (you have read the instructions!!).
my particular bike (2011 te 310 with q4 silencer), had/has a stumble just off idle. when you turned the throttle a very small amount from closed it starts to stumble and hunt, the smallest turn of the trottle will then sort it out and it starts to rev and pull. (the problem here is in tricky stuff where your feeding in the throttle slowly and in small amounts) you dont want to be closed throttle but you dont want to be accelerating, also if you stand up riding over the bumps or whoops in this throttle range the action of being thrown back and forward makes you open and close the throttle a miniscule ammount making it very hard to control the revs or the bike for that matter. imagine your in a rut, u wanna use closed throttle but not lose speed but u dont want to get any faster. its bbbbrrrrmmmmm baaaaaa bbrrrrmmm baaaaaaaa brmm baa brmm baaa, like a see saw, if you have a 310 you know how much engine braking there is and how closed throttle forces u forward with this engine braking and how when they do start to pull the puuuuuuuuullllllllll.
looking at jds maps and it shows that at 2200-2700 rpm(something like that) the fuel looks way too rich and the cures itself.
i left the idle circuit (green/blue) standard as is mine is set to 90 on ibeat and im not paying £35 to husky just to put it to 100!!! However, the green setting i leaned right off so it would correct the standard ecus overfueling at this small throttle opening. you can see from jds lights that you go into the yellow range quite quicky from green and the actual green range is quite small.
i set the yellow blue (transition timeing from green to yellow) to a lower than standard figure (think 2) this gets me into the yellow section of the tuner earlier so as not to stay in the lean portion any longer than is necessary. red i left standard at the mo and i have left the acc pump (red blue) standard mid setting. but from a starting point i would set this to 8 and eliminate it from the equation until you have all the other settings sorted.
remember tune it like a carb (so that would be main jet 1st, then idle speed,pilot circuit and then needle taper) in that order. leaving the red (main jet) setting standard means that you should be pretty much ok as factory should be close to ok on w.o.t. so then sort the idle and get a nice clean smooth idle which returns quickly and smoothly, sloooowly open the throttle and see what positions change the lights. then you can work out what needs changing and works for you.
having my bike ticking over on the stand and looking at the lights on the jd my stumble occured as it went between blue/green and green, so i knew fiddling with the green would make an improvement. if you wack the throttle wide open it isnt a smoothe rev up but has a momentary and i mean momentary hesitation if you do this more than a few times on the trot it will cough and stall with a bit of a pop/back fire.
BUT its a 4 stroke not a 2 stroke, you should be squeezing the throttle the open the majority of the time not snapping it wide open from closed. 4 strokes dont like this, carbed or efi regardless.
i think this issue on mine may not be helped by the fact that the tps needs resetting but at £35 a visit to husky it will have to wait,(unless they're reading this and gonna let me get it done for free, next time i go in there to spend my hard earned cash on parts and spares.) i have the throttle butterfly set open a little bit so as to minimise the engine braking, im going to set it back to roughly its position when i last had the tps reset and see if this makes the hesitation better.
mine is better but not perfect but i would rather ride it with it almost right than waste the rest of my life trying to get it 100%
My thoughts are that the jd tuner isnt a piggy back ecu so doesnt know the tps, the air temp, the coolant temp, etc etc, it just adjusts what it sees a little.
if you go for a richer accelerater pump setting you arnt changing the standard ecu acc/pump fueling as the ecu doest have an accelerator pump. the thing with the jd is its giving you a new option. an accelerator pump. the jd know/guesses throttle setting and when it sees youre going from idle to wot it chucks in some extra fuel for a bit. as the stumble occurs at low rpm and almost closed throttle it can only worsen the over richness if the acc pump function set too rich.
hope this has shed some light. obviously your ecu should be set to 100 100 100 as the jd says it doesnt adjust the richness or leanness to any way harmful setting. if your ecu is set leaner (like mine you probably wouldny be wise to lean it off any further) especially if in the road cruising part if the throttle range. if anything this is one of the areas you want spot on or a little rich.
of course every bikes different with different pipes, different air filters, different ambient temps, different cam timings(minute differences between standard cams and chains) different squish bands, compression ratios, valve clearances, different fuel, octane, fuel additives different altitudes, different humidity etc. so no two bikes will be the same what works for me wont work for you and viceversa.