Flooding simply means there is too much gas getting into the flow bowl. Gas flowing over the top, or coming out of the throttle shaft ends would be an indicator of a flooding situation.
Things to check:
- Needle & seat damaged - Perhaps the needle was damaged when adjusting the float. It doesn't take much pressure to damage the viton tip.
- Do you have the type of 4000 that the needle & seat does not thread in? If so, is the spring behind the needle & seat to hold it tight?
- Fuel pump pressure - Test your fuel pump pressure. Check your motors manual for the correct specification, but should be no more than 4 lbs.
- Check the float level. Both pontoons must be the same.
- Bad float - Heat up some water and immerse the float. Any bubbles indicate a leak. Shake the float to see if fuel is sloshing around.
- Float rubbing - The 4000 float has a tight fit. Be sure it isn't rubbing on the sides.
- Float sticking - Move the float up & down to be sure it isn't sticking. A worn float pin might cause this.
- Did the spring underneath the float get installed? It really needs to be there.
- Needle & seat gasket is cracked, or perhaps residue from the old needle & seat was left allowing fuel to flow around the needle & seat.
- Dirt in the needle & seat will cause the needle to stay open and leak fuel.
- Power valve, or power piston sticking which will allow fuel in when not needed. The economizer diaphragm should get pulled up at idle. Not something that is easy to check, but there needs to be vacuum going to the diaphragm.
- Power valve should have a gasket.
- Check the small orifices on the top of the float bowl. They need to be clear.
- Any gas tank vent needs to be open. Has the gas cap been changed with a non vented cap?
Fuel Flooding Into Secondary
While it may look like the Secondary is flooding, chances are good that the primary is also flooding. The primary is covered and hard to see when looking into the carburetor.