Here's something to look into, see below copied from the OC Hall of Wisdom. Check your wiring diagram to see if your bike also has this feature.
"Electronic Power Control:
KOTH: If you have the Electronic Power Control (EPC) system on your bike (all EU spec bikes 950/990 including early '04 USA), you can disable it by snipping the two wires that tell the ECU that the bike is in 2nd or 3rd gear. These are the gears in which the EPC limits engine acceleration to comply with European noise regulations. If you are not in Europe you likely don't have any noise tests to comply with. You will still want to remove the EPC valves from the 950's as they are subject to malfunctioning even when not connected to electrical. The connector for the gear sensor is #2 in the above photo.
yellow-brown = 3rd gear
gray = 2nd gear
FastEddy760: Pins Removed for Gear Sensor. It is easy, and this will help take the guess work out of the process.
1. Left side, follow wires from the gearshift and the side stand sensor (#2 in above photo).
2. Disconnect the plug, and put the side stand end to the side, it fits nicely over the flywheel cover, and out of the way.
3. You will be working on the end with the gray, yellow/brown, and green/black wires.
4. Use a small jewelers screwdriver inserted into the plug, and a little tension on the wire, to pop out the female leads for the gray and yellow/brown wires. Leave the green/black wire connector alone.
5. Cover the wires with shrink tube so they wont ground out.
6. Plug back together so the neutral switch will still work."
2008 KTM 990 Adv & 2007 KTM 640 Adv