| This should sort it.....
This just happened to me on my 998.
Check the fuel pump relay (little black box widget under the battery, next to indicator relay). Mine was corroded and goosed - replace, and smile.
Mine decided to play up when I unloaded the bike at Nogaro at the end of a ferry journey and 450 mile drive for 2 days on track - oh, how I laughed.
HUGE thanks to Flavio of the Ecole de Performance for sourcing me a new relay. | 
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