rough idle and low end, clears on top end

I have a 2000 Nautique with a GT 40 fuel injected engine. Last summer I replace the fuel pumps and filter (engine driven and canister); I don't run ethonal. At the start of the summmer I began to not get the quick start that I am used to, futher, my idel speed is missing and up to about 2500 RPMs the boat misses. If I accelerate past the 2500 rpm range the roughness smooths out and runs all the way through top end like a champ. Pull back down to 2500 rmp all the way back to idle I have the same rough performance. Unfortunatly my 9 year old skis at about 23 mph. When I restart after running I have to hold the starter on, it finally cathes up and starts. I put a can of Sea Foam in the gas with hopes to clean the injectors or dry up any water that may be in the system. I checked for water in the canister(no water or bad fuel smell). Changed the distubitor cap and rotor button as well as the plug wires (no coil wire came with the plug wires when I ordered). I am past my abilites of trouble shooting. I have read a little on the MAP sensor etc but do not know how to check these things. Summer is running out! hope someone can throw me a bone. Johnny