I'm not sure about the very loud noises coming from the bottom end, maybe someone else could address that, it may be somehow related to your issue. It sounds like the sputtering and dying is carb related, maybe spark plug? Check to make sure it's the
right spark plug and it's gapped correctly, that could cause loud noises. Fuel line clogged up? Is your fuel cap vent hose clogged? Dirty jets? Floats stuck? The fact that you changed the clip position and it made a difference may mean it's carb related unless it's something related to the very loud bottom end valve noise, not sure what that is or what problems it might be causing.
If your problem is carb and jetting related, here's a couple very good post on 2-stroke carb jetting adjustment. Maybe a good place to start after finding out what that loud bottom end noise is (don't think that's normal).
I found these posts pretty easy to understand. Have you repacked your exhaust? If it's a new bike to you, I'd put a new weisco piston and rings in it. The original KDX piston skirts sometimes fracture and break off into the engine. I'm sure you know to have kips valves adjusted. You can tell if you need new crank bearings by checking out the play after you have the top end off. Tolerences are in the service manual. Get a service manual.
http://www.thumpertalk.com/topic/347305 ... read-here/
http://forum.dirtrider.com/discussion/7 ... ng-faqs/p1