You need to dump the contents of each separator into separate glass jars. Check for water. Be prepared to see more water than fuel, if that's the issue. Remember - fuel floats on water, NOT the other way around...
When I had water issues, they wouldn't crop up until 15 minutes into a good run, sometimes later. What happens is that 1" of water, sitting just below the fuel pickup tube, will become a foot or more, when on plane and forced to the rear of the tank (think triangle). THIS WILL QUICKLY FILL UP YOUR SEPARATORS WITH WATER, choking out the fuel.
I could run, all day long, at the dock - the water stayed below the pickup tube. Only happened when I got up on plane.
If that's your issue, get a small electric fuel pump, rigged to a 1/4" plastic tube (ice maker line). It will slip nicely down the fuel pickup tube, going all the way to the bottom of the tank and bridging that 1" gap. Pump out 5-10 gallons from each tank.
Best way to isolate fuel issues is to rig up an outboard tank (3-6 gallons), with a transfer valve setup. Put it just below the fuel pump and run the engine off of it for a minute, to bleed the air, then go back to the main tank. Then go for a run, get up on plane, and as soon as engine starts to falter - switch to the temporary tank. If your problems vanish, you know it's fuel...
I am currently looking at an issue with the connections on the ballast resistor. Very similar symptoms. Check those connections, as well.
John
--
1987 32 Sedan Bridge
Twin 360s, Rebuilt 2006
Modified/Original Electronic Ignition
Raw Water Cooled
Catawba Island, Ohio