So, you are saying that someone has been into the intake manifold, there are signs that the gaskets were replaced….
I am suspect when I see things like this, always "wondering why"….
Generally speaking, an intake manifold leak/reed problem will be more evident at lower speeds. You mention the engine "runs OK" at lower speeds "but needs a lot of choke". Are you running the boat on the water, or in a bucket? There is a bogging problem at higher speeds, but the engine surges back to life when the throttle is reduced…
You mention that the carb/linkage is properly synchronized, but the symptom you mention makes me think something is off with it. Did you actually remove the high speed jets? Did you use the proper jet screwdriver?
How about the distributor belt? Is it properly indexed on the flywheel/distributor? If this is not set up properly, it might cause the symptoms you describe.
I guess at this point, I would probably start over from step one, can’t remember if you checked compression…
Back to your original question, it is surely possible that someone made a mess when they had that intake off. New gaskets are not expensive, just an investment in your time to pull it off and clean the gasket surfaces properly and check the reeds…Generally speaking, the new gaskets should be installed "dry".
I am trying to remember the story on this engine, but am assuming you bought it and it has never run correctly for you, is this the case?

It’s been about 50 years and my memory is foggy as to the symptoms, but I remember on a V4 60 HP, some running issues due to a small hole in the rubber fuel pump diaphragm. I don’t think this is your problem, but an easy thing to check and/or replace.
Dave

Uncontrollable runaway is usually a result of revving it up in neutral or out of the water, or other no-load conditions such as a busted shear pin. However, as I read your story, you seem to indicate you had it on the lake. So, I dunno–was it in gear at the time?

Other than that, your symptoms scream out "Too lean". OK, back to the carburetor for the 10th time. Are you SURE the high speed jets are absolutely clean? Are you SURE they are the right ones?

If you are sure of the above, then are you SURE the belt timing is correct? And are you SURE the carb/distributor linkage is properly synchronized? If not, it absolutely will cause just what you are describing. My honest suspicion is that this is the problem (?)

I seriously doubt it is the crankcase leakage that you are suspecting. If it were, it would show up as poor running at idle, not at high speed.

One last thought–does it run better with the hood off? Missing parts from that extension kit will cause it to smother with the hood on.

OK, thanks for the info, so the engine did run OK before making the long shaft conversion….
Everything you describe screams out some sort of fuel problem, or belt/carb/distributor synchronization issue. Although, never say never when it comes to a spark problem, sometimes they can sound like fuel issues.
I am trying to remember whether this engine has battery CD, or the conventional 12volt automotive type distributor ignition set up. Am "guessing" it has the conventional distributor set up.
You said in your first post that "the intake has a lot of gasket going on", what do you mean by that? Your latest post indicates the intake has not been messed with….
I’m guessing intake air leaks are not an issue if the intake has not been messed with. Spraying the WD40 around the intake can fool you, because it is really being pulled in through the carb, not a leaky intake gasket. Generally speaking, you will see fuel residue on the block if there is an external air leak issue.
I like Frank’s idea about running with the cover off. Let us know how the engine ran away on you, were you revving it in neutral?
I agree with Frank, my next step would be to go through the timing belt and sync set up procedures….
Am glad to hear you are purchasing the correct jet tool, it is worth the expense…