I'm seeing a major engine components/overall powerplant mismatch here, and on several levels (actual parts chosen, specific part type chosen, and I suspect part setup when installed). Looking at what you are working with, your unfortunate real world results seem about right to me relative to the overall combinaton.
You need to be willing to make some substantial component changes in order to see a dramatic improvement, including induction, exhaust, camshaft, I suspect cylinder head port work, and I bet valve train geometry (which significantly affects cam timing).
LO
LO give me your opinion on where to start then. If you're seeing something in my parts list that seems off I'm all ears.
I'll take a minute to explain the parts chosen, then I'd love for people to chime in and make me aware of the error of my selections, and their suggestions towards better parts.
Here we go.
The mission: Make the boat faster. (Isn't that what we all want?)

Limitations: Full engine enclosure with a flat sundeck for the hunnies. So, no headers. Lightnings MIGHT fit, but man... the cost. Also, it has to be reliable. I want to get 5-8 seasons of use out of it before rebuild.
Engine Design: Jet boat performance is a result of torque. So, lets make lots of torque at lowish RPMS.
How to make Torque: First.... make it big. I went with the 521 because a 4.3" crank was a large as I was comfortable with for longevity. Same with the .030 overbore.
Next, a dual plane intake is known for its low-ish RPM torque building. I was already running the Stealth, so run it, and save a few $$.
Carby selection says that you go Huge for big RPM and big horsepower, and you go smallish for low RPM response and again, torque. I chose the 850 as it falls right in the middle of those 2 requirements.
I was also already running the D0VE C heads. There are thousands of builds out there making serious power with these heads. So, some mild port cleanup and a few more $$ saved instead of SCJ heads.
Cam selection. This is where I turned to my engine builder for his advice. He suggested this cam, as it was designed for strong midrange torque.
exhaust we covered, I understand these logs don't provide great scavenging like a well designed header, but they are a necessary evil.
I could have built a maximum effort, high horsepower, high RPM fire breathing monster, but it would have REQUIRED headers, SCJ heads, bigger cam, single plane manifold, and bigger carb. I tried to choose parts that would build a stump puller instead. Couple that with an AA impeller and the intended result was to get good performance at lower than typical RPM's.
So, I need help from the peanut gallery to help adjust my recipe. Something is clearly off. And now that you know my intent, I'm all ears as to how to get this boat to move faster. After all.... it was a 63 MPH boat with a 460, same intake, heads, 750DP and an aggressor 9 vane bowl with aggressor A impeller.
Lets hear those thoughts and ideas.