I recently bought a 1997 Yamaha Big Bear.  The electric start wasn't working.  I found out that the starter clutch was shot.  I drained the oil and quite a few metal shavings were in it.  Once I saw this I flushed motor oil and gasoline through the engine until metal was no longer coming out.  Since then I have changed the oil every five hours or so of operation.  I still get fine metal shavings in the oil filter, although less each time.  The motor still starts, runs and idles fine, but i'm starting to see a bit of smoke at start-up.  

My plan is to perform a top-end rebuild and change out the starter clutch simultaneously.  While the engine is opened up to perform these tasks I will thoroughly flush it out with gasoline and oil and compressed air.  

I'm a novice at this kind of engine work so I'd like to avoid a complete rebuild?

Questions:

1: Will this plan do an adequate job of removing contaminates from the engine?  If not, what would you advise?

2: Are there specific things I can check for damage while I have the engine opened up this much?