I lean seized my KDX a few months back. Same scenerio, just rebuilt + in process of breaking in. On a straight I gave it a little gas and it bogged out and died on me. The intake boot ripped, letting in all kinds of air, and so it lean siezed. The bike could still be kicked over, although it was very easy.
The piston partially fused to the (freshly plated!) cylinder wall, and the aluminum fused right over the rings. Good news is, I didn't need to re-plate or even get a new piston or rings. Just cleaned it all up with some 300 grit sandpaper and a de-burring blade and it was good to go. I've got about 30 hours on it since then, and even with a small chip in the plating it runs super strong, better than new.
Maybe you lost a circlip? If you used a Wiseco I wouldn't doubt it, those things are a PITA to get seated completely.
I'd also clean the carb out really good, making sure the float isn't hung up on anything and all the jets/passage ways aren't clogged.
Best of luck, I hope it's something small. :thumb:
PS Just re-read your post. Did you go through heat-cool cycles with the engine while breaking it in? You are supposed to ride it easy for a few minutes (until warm) then let it cool completely. A few times through this and it's good to go.