First thoughts, choke staying on?, sticky float?, junk in inlet to needle/seat?, junk in carb inlet screen (do 1409's have that?), wires on coil, cap & plugs tight? Spark plug condition? Tank vent? Anti siphon valve?
Here is the "book" on the 1409
http://www.edelbrock.com/automotive/...ers-manual.pdf
At those rpms you are on the primary fuel circuit of the carburetor. Which varies your fuel according to vacuum and throttle opening.
To try to correct any potential vacuum leak snug down the carb to the base gasket. If you find any loose hardware you might be done. If that doesn't work try a leak test by running the motor and shooting bursts of carb cleaner at potential air leaks such as the base, the choke shaft & the throttle shafts where they go into the carb body.
If you disconnect the throttle link to the helm you can control your throttle at the motor. Do that it's easier for this check. Try the carb spray at idle and above 1200 rpm. It will probably need to be checked at the running rpm (over 1200) because the idle circuit starts to give in the the primary fuel circuit at around there. Your issue is above 1200 so concentrate your testing there.
How does it do at full power?
if that doesn't work see if the new fuel water separator is bad, maybe try another one. Might just get one anyway. It was changed and now the boat acts differently.
