Just something else to look at, using a spark tester that lets you see a 7/16 gap test the spark as soon as it quits. You could have an intermittent issue with the CDI that is killing the spark after a few minutes.
Do you have a back up tank, or can you borrow one? I would want to run this motor on a completely seperate fuel tank and hose set up to eliminate your boat tank, vents and hoses.
Don't rush to pull the VRO off yet, when it is running for you pump the ball up and see if it continues to run, if it does then go ahead with your fuel pump swap, If it still quits it isn't the pump. If you have to swap the pump, look for the fuel pump for the same year 48SPL, that was the non-VRO model for that year.
Do you have the newer hoses that are able to stand up to the alcohol in today's gasoline? The new hoses are typically gray and are marked as ethanol safe. I have seen the the old black hoses deteriorate internally and find their way into carbs, even ones that have been recently cleaned. When you had the carbs off did you try to blow through the inlet port to see if you had free flow into the bowl?
Check your onboard tank for a mud daubber nest in the vent hole, it's that time of year and that would cause problems like you are expereincing. Try running the motor with the fuel cap off so you know the tank is vented.