Can you check the FI codes on the bike?
 

My r1 you were able to get codes that tell you whats wrong. Does the f4i provide this? My fi light is on the bike runs fine just seems extremely under powered. I have a hard time clutching a wheelie on the back pegs with stock gearing.

Any input?

Anyone?

Yes you can, under the seat there is a jumper plug use a paper clip
jump the connector turn on the key the fi light flashes the codes.

I tried google imaging it but nothing.. by chance do you have a pic? along with the list of codes?

x2 looking for this as well

The jumper plug is a small black, flat 2 wire connector under your seat, somewhere around the ECU. It isn't connected to anything, so you should see the 2 pins inside. Stick a paperclip in it, turn the bike on, and the FI light should start blinking. The codes are in the service manual, I can't upload the image of them. Find out how many times it blinks and i'll tell you what your prob is.

OOO ya. I know what one it is. My buddy kept yelling at me saying that is why the bike wasn't running because this connector wasn't hooked up lol.

Ill do it monday. I gotta work all day today.

Code I get in sequence is 129.

Have you tried to reset the ecu to see if the codes come back?
Disconnect the battery for 30 seconds and see what happens.
When you read the codes were they long blinks or short ones?

There all short.