FI (fuel injection)... just a heads up.
As far as why, the pair valve itself is just some plates blocking off air... now getting to them you may have disturbed the ECM wiring that runs from the battery area under the seat to the top of the engine on the right side there. The FI light remaining on may indicate the system is not active (which I'm not sure if the bike would even fire sparks if that were the case). The fuel injection system receives commands from the computer to allow more/less air in, more/less fuel, and when to ignite spark plugs...
I'd check those wires.