broken shift shaft

This is the first story I've heard of it happening to a KDX, not the first with other bikes though. Check out justkdx.dirtrider.net and under tech tips it'll tell you how to set up the powervalve.

Sounds like you had the chain way too loose, or worn sprockets/chain or combination. I'm not sure if a case saver would have helped in this case but they are worthy investments for when a chain lets go.

Regardless of wherever you get your KIPS setup info, make sure after you're done that it actually works they way it should. With the pipe off, look up inside the exhaust port, manually activate the KIPS using the nut under the slotted cover on the LH side of the cylinder.

Make sure the subport drums rotate in sync to the relative same position....both when fully opened and closed.

Make sure the main valve raises when the KIPS is activated.

More likely to have a problem with subport drum timing if something has been put together incorrectly.

re: chain breakage and subsequent damage.

No. Not common.

The bike DOES have the chain slipper on the swingarm, doesn't it?