rough idle and bottom end, clears up top end?

I have a 2000 ski natuique with the GT40 fuel injected engine. I don't use ethonal fuel, I replaced both fuel pumps (engin driven and the one in the canister), I changed my spark plug (did not change the coil wire), changed the disturbutor cap and rotor button, and checked the canister for water (none!) Here is my problem: Idles rough, misses up through about 2500 rmps, then clears up through top end, runs like a top. If I back back down it start the rough stage back through idle. The boat will no start with a push of the buttom, it turns over and finally catches up and starts. I am past my knowledge and need help.......help!