Sorry to hear you had to take the motor out (I remember the thread when you were having difficulties). .009 is fairly tight, but the motor should still turn over even with .009 clearence. I would say piston to cylinder wall clearence would more likely cause a starter to have a hard time turning over an engine if the clearences were too tight. Are the rod's facing the right way against the crank journal? Every rod has a groove on one side of the big end, and that groove has to be facing against the crank journal, not against the rod opposite it. Check that, many people make the mistake of not facing them the right way, and crap happen's when this mistake occurs. (Turn a bearing, poor oil control etc.) Also check the thrust bearing clearence for the hell of it as well while your at it. Myself personally....I suspect piston clearence problem's, or the ring's were installed wrong.
What kind of rod's are you using???
Good luck man, and hopefully you get her sorted out. Keep us posted.
Who built the engine????