I had/have a similar problem. In my case the fuse for FI kept blowing in the fuse box accessible under the seat if you haven't checked that. From there something else blew which is pointing towards the ECU as the fuel pump & injectors are also not getting power. So far Yamaha says the ECU, Ignition lock, keys, must all be replaced. I also don't have a red key.. Also having some things checked on the bike still, but sounds like a similar problem. I somehow believe the fault is related to the fact that the bike cuts out so frequently while driving due to the sluggish fuel delivery and all those spikes/ drops had adverse effects on the ECU.. but that's just my opinion.

I'll let you know once I know more.. Please post again once you've made a conclusion on your side..