In the manual I have it only mentions the KIPS when taking the engine apart. Is it possible to clean it without taking the engine out of the frame or rebuilding the top end?
You can remove the power valves for cleaning with the engine still in the frame, but you must remove the cylinder head to remove the sub valves. So you you will need a new head gasket. If any of the other gaskets are torn or damaged during the tear down haveing a top end gasket set is nice. If you have the factory service manual its description lists the steps to do a compleate top end service with the engine in frame. Just beware that when the manual refers to right or left sides it is as you are seated on the bike. Look on the kdx rider.net site for a pictoral showing how the steps look as it is disasembled.
Actually, I'm pretty sure you've got to remove the cylinder, not just the head, to do a KIPS cleaning job. I'd consider a piston/rings/upper bearings/clips while in there.