My 03 did the same thing in its first year. I had a set of yosh pipes and a pc3r installed. They did not cause the problem. Here is what mine did: Heading at full steam into a max lean corner, my RC just bogged and shut off momentarily. It was like someone hit the reverse thrust button. One second you are setting up for the hard left corner and suddenly massive engine braking occurs and I start heading wide. Not good. So I payed attention to what was causing the glitch. It eventually got so bad that nothing really seemed to stand out as the culprit.
I limped it to my trusty mechanics house. He works for the shop where I bought the RC from. He showed me how to pull the engine light codes with a simple wire. The dash showed a code 14. I got the service manual and looked up that trouble code. It was a vague description but it ultimately lead me to the rear cylinder injector. The protocol was to disconnect and reconnect the wiring to that rear injector and retest the bike. Ever since then, no problems at all.
My advice to you is this: If the FI light came on then there is a code in the computer's memory that needs to be cleared. That code will give you or the shop the bike is at a good starting point. Chances are it is just a loose or dirty connection that simply needs to be pulled apart and reconnected. Mods and the way you choose to ride your RC has little to do with an FI light coming on and bogging you bike at those rpms. You are doing the right thing by getting the problem documented before the warranty runs out.