Is the cylinder, piston and such back on right now, or is it still just the connecting rod sticking up out of the crankcase?
I have a few ideas on it. You could clean it the best you could and hope for the best.
You could remove what rust, leaves, etc. you can from the crankcase, then remove the engine from the frame. After the engine is out, you could use a lot of two stroke oil, or maybe kerosene, etc. to try to rinse the crankcase out as thoroughly as possible, then leave it upside down to drain for a while. A small amount of excess will cause it to be hard to crank for a few tries.
If you really want to do it right, then a thorough inspection of the crankshaft bearings is in order. This usually means splitting the cases. From your response, I suggest that you DO NOT attempt this yourself. Though it is not cheap, a professional shop sounds like the best bet for you as far as splitting the cases. There is a lot of difference between fooling with the top end (cylinder, head, piston and such) compared to fooling with the bottom end (transmission, splitting cases, etc.). I do a lot of work on my bike, but I know my limitations. Clint Eastwood - "A man's got to know his limitations." I know not to fool with the bottom end...or Dirty Harry.