I have a 96 502 mercruiser mag mpi and it is having fuel problems. It has a new mechanical fuel pump and also a new high pressure fuel pump in the vst chamber. The boat will run good for 45 minutes to an hour but when you kill it and let it set for a little wile it will start and idle for about 5 minutes and then starve for fuel and eventually die out. I'm not sure where to go from here.

Sounds like vapor lock

Odd how some (same fuel system) have the issue and others do not. Other than engine room venting (temp.) I can't put my finger on it.

Fuel pressure relief valve. Without engine running. Turn on key then turn off. system should hold close to 50 lbs. Had replace this on 1996 350 mag mpi gen plus. Your motor uses same one. The 350 had a Schrader valve like a valve stem on end of fuel rail. I used a cheap dial face air pressure gage to check it.. I found a couple on ebay and snapped them up. If you cant find one Believe it or not. A Honda civic uses the same one.

There is an internal diaphragm at the top of the VST chamber that will deteriorate and cause the issue you describe. You need to remove the VST top, and flip it over. You will see another cover with 3 screws that need to be removed and there is a diaphragm within that will likely be shot. Replace this and your problems should be solved. It is often confused with vapor lock but is not. Basically when this diaphragm ages and breaks down high pressure fuel will percolate through this vent into the manifold. It bleeds down rail pressure and floods the motor.

Genuine Mercury & Mercruiser parts. VAPOR SEPARATOR TANK, SN & Below (See Note)

I just pulled them 3 screws out and the diaphragm looks the be in good condition no holes or tears.

replace it while you have it apart.

Interested to here what you found out?? Here is another pic of your vapor separator tank with fuel rail and pressure regulator. Got that from cp performance sight. The regulator drains back to vapor separator tank

Trey did you check fuel pressure as indicated above by Veloc?