I have a feeling your TPS is to blame, Throttle Position Sensor.

In 2006/7 there was an official recall by Yamaha to have them all changed free of charge, it could be your bike might fall under that category, probably being a 2007 build that only got sold in 2008.

To be sure please remove the TPS and read the serial number then send Kev a pm with this number and he will be able to tell you for certain if the TPS is one of the faulty ones in which case you can go back to any official Yamaha dealer and ask them to swap it for a new one.