My 11 can be difficult to start or it is a one kick affair. I never know which way it's going to be when I stall it or shut it down. When I stop, I try to do so on the top of a hill or a descent.
Absolutely needs to be in neutral. Raising the idle may have made the biggest improvement in starting. Adding the GYTR offroad flywheel made it easier to start too.
Also, there is a video from Yamaha
about starting the FI bikes. Watch it and take notes. Of particular importance is not kicking the bike too hard. If you kick too hard the engine speed will be too high and will override the decompression springs and make it harder to start. I'm 6'4 and squat 300+# weekly and really feel like I'm resting my foot on the kicker when I start it. It still starts inconsistently but it is better than before when I used to kick it like it cheated at poker.
I'd like to try making changes electronically. If you do, please let us know what you did.