3 liter mercruiser fuse problem

[bill k miami]

my 1999 bayliner/3 liter mercruiser ignition fuse blew under load in biscayne bay. the wire from the terminal on the fuse panel that blew goes to my battery terminal on my key switch. we were traveling about 35 mph and the motor seemed to just turn off. i would replace the fuse and after a few minutes the new fuse would blow again. before the trip i replaced the alternator, the plugs, the dist cap and rotor. it was the first trip in this just purchased boat. in my driveway the motor seems to run fine. the alternator is putting out about 14 volts while the motor is running. the fuse did blow again a few times while trying to start the motor this weekend in my driveway. the motor would seem to sputter on start up and the same fuse would blow. after there was enough fuel in the line, it would start right up without the fuse blowing. i put the old alternator back on and the voltage reading was about the same. all the wiring seems fine. i also replaced the battery and replaced the terminal connections as well as clean all the ground points. the starter, slave solenoid , and safety switch seem to be working fine. what should i check next???? thanks