I have a 97' gen 6 502 mag mpi, ran fine after coming to a stop dropping off passengers. After leaving the dock, it started to stall out once it hit 3500 rpms. I backed off the throttle, and it idled fine. Attempted to try again, same results. cruised on over to the launch ramp under 3000rpm no problems.
Took it to a shop, and said we had 40psi of fuel pressure, so it would not be fuel related.
He did a leak down test, found a cylinder leaking up to 50%, but he could not tell if it was coming from the intake , exhaust or cam? He said the only way to tell was to start tearing it down and go from there. When I asked him if he had changed the fuel filter, he mentioned, that usually never fixes the issue, and most likely just needs to be rebuilt.
Anyone else have this issue, if its not fuel related, could a bad top end cause this?

Get your boat and run away from this guy

Pull the fuel filter and dump the contents into a clear jar
It way very well be the filter or something else fuel related, right now no one knows and need some testing. Place a fuel pressure gauge on the rail and take it for another ride. Reading pressure with key ON or on a hose doesn't tell much other then pump and regulator are working. Under load it needs a lot of fuel so it could be a restriction.

Already picked it up, going to do the fuel filter.
I'm wondering if its just the ethanol in the fuel, our state uses ethanol in all our fuel

I have had fuel lines come apart inside and restrict the fuel. would run fine up to 3500-4000 and then lay down. as stated change the filters and then run it up to speed till it drops off with the pressure gauge on it and see if psi drop off at that point.

Not sure which seup you have, but I had the micron filter in the vst tank get dirty and caused what you described.

Replaced the fuel filter, looks like sand though

I have the cool fuel system

I don't like the color, it should be clear