From your description I still cannot see the problem in the engine. If the engine was low on power you would notice a difference at all rpm ranges. Being your problem is with just starting out and good throughout the rest of the power range I would still suspect something in either the clutch or transmission. The rollover with engine still running would not hurt the head or rings since this is where the oil went, the roller bearing and needle bearing will not be affected too much at all since it wasn't run too long inverted. But the clutch would take the biggest hit since I believe that engine is basically the same as the TRX250sx for it is a wet clutch system and they don't like not being soaked in oil. It's great that you have a spare to swap out. You can always go through the old one and build a killer engine if you ever felt the need for more speed .
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