Papa,
My shop manual is for the 2008 models so I'm not sure how applicable this may be, but here goes.
If you are getting a constant flashing gear position and your MIL lamp (FI lamp) and engine coolant temp lamp are off and you cannot start the engine then then you need to check the PCM power/ground line. The procedure requires that you pull the PCM's 33P gray connector (under the rear fender cover) and measure for ground on pins B10, B13 and B22. These are all green wires going into the plug. As you are looking at the gray connector face the pin in the upper right hand corner is B1, increasing as you go to the left (top row goes from B1 to B11). The second row goes from right to left B12 through B22, etc.
After checking for grounds then look at pin B1 (black and red wire in this
slot) for battery voltage.
After that reconnect the gray connector and remove the black 33P connector. Following the same numbering sequence (except all of these pins are A) find pin A4 ( top row, fourth from the right). This wire is black and white and will have battery voltage whenever the kill switch is on (center) and the key is on.
If all of those items are good then you probably have a PCM problem. Not necessarily a bad PCM module but maybe a loose wire, etc.
This could become a complicated troubleshooting effort. Since your bike is under warranty I would suggest that you haul it back to them and have the dealer fix it. When they are done ask them to explain exactly what was wrong and point out where the bad components/wiring were at so you know if this comes back.
Good luck,
Booma