Not really sure what you just said beyond you replaced the fuel pump.  Does the engine die when you try to idle after startup and it is cold.  Will it restart?  Does it run ok after it warms up?  If so, when the engine is cold, you can hold your foot on the pedal and keep the idle higher or set the idle speed up.  The only issue with setting the idle speed too high is  when docking, the boat may be faster than you would like.  You can take care of that by putting the reverse bucket partially down.

I have a jet boat with a 460 Ford engine in it and I just replace the Holley pump to read Holley pond the boat when I put it in the water starts to shut off after a few seconds of running how do I adjust that

I had a sleek craft back in the late 70's  when I set the boat on the water off the trailer it would not start.   EVER.....
I would have to load it BACK on the trailer, pull it put of the water.....start it on the trailer THEN put it back in the water .... Did it every time or the 2 years I had that boat .....

I never could figure out that weirdness..