98 SEA-DOO GS- Will not power up in water!

I am working on a 98 sea-doo GS and it is driving me crazy! A customer brought me this ski with a lean and blown cylinder, I proceeded as always with the upper end rebuild,i even went through the carb and it was terribly dirty inside! I had the cylinders slevved and bored to fit factory size pistons as the cylinders were ok, I put the ski back together and it will not power above plain in the water, I pulled the ski out of the water and checked it out it seems to power up fine, as they all do out of the water! I havent used this machine shop before could there be something wrong with the sleeve incersion in the port line up? the bolts went in ok but one sleeve was off less than 1 thousandths? man im stuck I just cant see any visible problems! THANK FOR ANY HELP!!!!!!!