You should be able to get a "reading" yourself off if it. The flashes (just like checking your car's ECU) should tell you the problem. You might just have some corrosion on the electrical somewhere, but I'd start here.
FI CODE FLASHING : Suzuki GSX-R Motorcycle Forums: Gixxer.com
GSXR Fuel Injection (FI) Code List:
C14 - THROTTLE POSITION SENSOR
C15 - ENGINE COOLANT TEMPERATURE SENSOR
C21 - INTAKE AIR TEMPERATURE SENSOR
C22 - ATMOSPHERIC PRESSURE SENSOR
C23 - TIPOVER SENSOR
C24 - IGNITION SIGNAL #1
C25 - IGNITION SIGNAL #2
C26 - IGNITION SIGNAL #3
C27 - IGNITION SIGNAL #4
C28 - SECONDARY THROTTLE VALVE ACTUATOR
C29 - SECONDARY THROTTLE POSITION SENSOR
C30 - SECONDARY THROTTLE CONTROL UNIT
C31 - GEAR POSITION SENSOR
C32 - INJECTOR SIGNAL #1
C33 - INJECTOR SIGNAL #2
C34 - INJECTOR SIGNAL #3
C35 - INJECTOR SIGNAL #4
C41 - FUEL PUMP CONTROL SYSTEM
C42 - IGNITION SWITCH SIGNAL
C46 - EXHAUST CONTROL VALVE ACTUATOR (1000 ONLY)
Found this too so maybe this will help
On the K3 1000 there is a six pin connector in the trunk with a rubber boot covering it. Cross the black wire with the white stripe with the white wire with the red stripe to go into dealer mode. Amen.