Big Bear Starter Clutch

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?  

Hi Bigbear ,when you see the starter clutch check the idler gear for wear your metal filings may be from the one way bearing slipping on it . best to change the idler gear and the one way bearing other wise you may have to open again.