If they pulled proper RPM the day before the floscans were in and now they don't and there were no other changes, I'd sure look first at the floscans/related installation issues.
Onward from there -
question is at what rpm do the secondary's open up?
Quadra Jets, like virtually all oem carbs regardless of brand used on production street engines, open the secondaries based on engine load, NOT RPM. That's why you can run the engines at say, 4000 RPM with no load and the secondaries may open only slightly if at all. Therefore, there is no way to really say what RPM they should open. They should open when the engine needs the additional fuel air, not before. That can vary depending on a variety of issues.
Ideally, when a carburetor is set up and working properly, you should never "feel" the secondaries come it. The old hot rod thing of "Wow, feel those secondaries kick in!" means you have a problem with the set up and the engine is not producing the power it should be across the rev range.
The fact that the secondaries are opening indicates that sufficient vacuum is being applied by the engine across the secondary air valve to require the additional fuel/air. So the question is, why is the RPM not continuing to rise to the 4000-4400 range that it should.
What follows is based on an assumption that I gathered from the post (perhaps incorrectly?) that both engines are doing the same thing.
Yes, it may very well be fuel related (floscan installation) but if you described these symptoms without the floscan installation, the fact that the secondaries are remaining open and drawing fuel would lead me in a different direction initially.
Usually, if there is a fuel starvation problem, the eng will pull up until the carb bowls run low on fuel. Then, if the throttle is held fully open, the rpm will drop off to some stable level but seldom will their be enough fuel for the secondaries to remain open. Since that isn't happening, the first thing I'd consider, if the engines used to pull to the proper RPM is a dirty or fouled boat bottom OR a lot more weight in the boat than used to be there. If both engines are doing the same thing, it's unlikely that both carbs/fuel pumps/etc went south at the same time.
For that reason, suspecting an engine problem - both engines doing the same thing - would not be first on my list. However...
I assume there's no obvious misfiring going on, right?
Did anyone rewire the spark plugs with new wiring before this behavior started? It's easy to misswire cylinders 5 and 7 on these engines. The bad part is that they will run fairly well this way and actually sound OK. Of course they will NOT produce the proper power. 5 and 7 can also crossfire quite easily if the wires are not in top condition.
It sounds as if no one has messed with the carbs but has anyone worked on them and perhaps changed the airvalve settings?
If you brought me a car with these symptoms, the first thing I'd check wouldn't be fuel - it would be timing and then for an exhaust restriction. But the fact that BOTH engines are doing this make it hard for me to think it's engine related.
Certainly, the fuel system is common to both engines but it seems unlikely that a fuel starvation issue could still provide enough fuel to sustain operation of both engines at 3700 RPM. I have heard that floscans can cause or exacerbate small bubbles in the fuel flow which might be related but I don't have any experience with trouble shooting them. Maybe that can cut the fuel volume a bit but not all that much. There are folks here with flo-scan experience that can help more on that specific issue.