Sounds like an injector is not operating properly.
+1 = Last time you ran SEAFOAM or something similar through the system? Have you left untreated gas stored in the tank? Ehtanol is a KILLER in a fuel system when left standing introducing moisture hence the above point.
Have you checked or replaced the fuel line for obstructions or kinks? Disconnect the fuel line and see if your getting debris out of it like hose rot.
VJ is right, you need a load test on the Battery in addition to ensuring contacts are clean. Weak batt could cause headaches at idle for ECU.
Plug wires / Idle set. Wires may look good but another rider just resolved similar problem by replacing wires and ensuring idle 1000 +/- 50.
Fuel pump pressure, I believe should be 49PSI. Need to check that but the flip side of that if no obstruction in the line is when is this caution coming on? When the pump continues to run past the 3-5 seconds. Just for clarificaiton, your saying when you turn it on the pump continues to run past 5 seconds prior to starting then you continue to hear it?
If you must, remove the tank, open it up and inspect the filter and fuel return line on the pump.
I would start with battery load test and seafoam while your finding a pressure guage to check your fuel pressure.
2011 White Vision - Nuvi 550, Lowers, Lloydz 2nd filter, Vic perf filter, CB/Icom, 96 Brake LED's, Clear Signal lens/Switchbacks, VIC Hwy Pegs, Stebel Horn, 7Jurock 15" Shield, PCV, Lloyd ATS and Variable intake, Ness honkers
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