This sounds like a fueling issue to me e.g. not enough pressure in the system etc. I have two FI bikes the scrambler and an SR400. SR is kick only, so I use a little trick I used to use on my old VW Squareback FI. I turn the key on and off multiple times before starting the bike. Each time you will hear the fuel pump whirl and pressurize the system. This ensures that there is sufficient fuel pressurized.
This will not fix your issue, but maybe make it easier to start. Good Luck.