How to flush your bottom end out after a burn down?

That motor needs to come out and be torn down. Split the cases, it takes more time but doing it right the first time will be faster and more cost effective in the long run.

I have to agree with BigHoe. I wouldn't be able to sleep without splitting the cases. I would check those crank bearings as well. Roll them over and feel for any harshness or noise. May save you alot of $ down the road. I have burned down my share of 2 strokes and that's the worst one I have ever seen. I can't believe the piston didn't just break apart. Amazingly you shut it down when you did or who knows what you might be looking at right now. Split the cases, replace the crank seals, and do it right. You'll thank yourself later trust me. I've split the cases and completely rebuilt 2 M1000's and it's not that bad. Check those crank and rod bearings good. There was alot of metal that went through there. I bet at a minimum you find the rod bearings slightly scarred. You can send your crank to SLP to have them replaced, that's what I did.