Does this occur only at idle, or do you get these symptoms under power?
Are the plugs wet or dry after this happens? If wet then likely a flooding issue caused by carb needle or float.
If occurs at idle only, you may just need to adjust the idle, and idle mixture screw.
I recommend you download service manual 24 from documents and see "carburetor malfunctions". For adjusting idle mixture screw, see pg 4B5- Timing follow steps 3-8.
If this is occurring at power then likely a carb or fuel issue.
Have you ever had the carb rebuilt?
Are you sure that your gas is good, no water?
Why did you replace the water separator twice?
To check the manifolds you will need to remove them. You will need a manifold gasket. Let us know if you want to do this and we can give you some pointers. Not hard, just heavy.
2006 Bayliner BR205
A1 Gen 2 1.47
5.0 carb engine