Chad,
It sounds like something is routed incorrectly, but it could have been me misreading your post.
Just to keep it simple, here is what you should have...
From the jet pump to a valve you can adjust (typically just a 3/4" gate valve).
from the valve to a standard tee, set up in the bullhead configuration (water enters through the branch),
from the outlets of the tee to the log manifolds closest to the bottom (2X)
from the outlets of the log manifold (which will be the higher ones) to the front water pump bock off plate (2X)
From the thermostat housing (sans stat) to the bottom of the snails/risers.
The temperature sender for the engine should be located somewhere in the intake manifold in the area of the t-stat housing.
The inside diameter of the riser water fittings should be no larger than 3/8", too big and you will move way too much water, I have done these with as little as 5/16".
These fittings can have the inside bore reduced in many different ways, you can even install a stainless steel nut in the hose and hose clamp it right before it goes to the last barb connection (redneck, but works great).
Chances are that something is plumbed incorrectly or the wrong fittings were used.
Chad, sounds like you have the hoses from water outlet(t-stat housing) and water pump plate mixed up. Incoming water should flow from pump to "T" to logs to water pump plate. Water leaves via the water outlet on manifold and goes to bottom of snails. There should not be a t-stat in use unless you have a specialized setup designed for one.
I think I agree with you, but I couldn't quite make out the post...
Typical jet boat does not use one.
Or really need it.
This may be one reason you can't get to your target temp, the temp sender is measuring incoming water temp, not the outgoing water temp.
BTW, there is no reason to try to achieve the kind of temps you are accustomed to seeing in a road vehicle.
While I agree, I think there may be something wrong.
There is no comparison between a boat with open cooling system and the closed cooling of a car or truck.
No truer words were ever spoken.
You're a better man than me if you could decipher that ...

GT