I have 2 je bowls that are different, 1 has a round plate mounted where the fins are .The other 1 has no plate or holes to mount 1 to. Looks like something added to fill bowl . Any one tell me which 1 would be best to use. Also has anyone ever had a shaft welded and turned back to specs. on the bushing end where they wear.Does any one make a oversize bushing so you can turn down the shaft (like a over size rod or crank bearing) how much wear is to much to run.

The plate is called a stuffer plate (someone added it).  If the bowl with the plate fits without hitting the back of your impeller then use that one.  Its there to try to keep the water flow going somewhere useful (through the bowl) instead of swirling around behind the impeller.

 Give Tom at Jet Boat Performance a call (805-466-4719), he can tell you how to check the clearance.  And maybe explain it better. 

Jeff you did fine on your own , good info above Streetfreak !