Lining Up The Main Exhaust Valve...

what year/model is the kdx?

You should probably remove the rod and the valve to clean it and remove any carbon. Iirc, above the exhaust port on the outside of the cylinder there is a plug that needs to be removed to gain access to the main valve.

When the rod is in, all three valves should be closed. They should all rotate simultaneously to a fully open position (seen through the exhaust port) when the rod is pulled outwards.

Removing the cylinder will make things easier for you. It sounds like you will need to anyway

Cheers :)