So if you have two inboards, Both Closed cooling, A lot of the parts that are new. One is overheating/getting hotter than the other.
What does the incoming water system look like? Do you have a strainer system where the water comes thru the hull?
Is it clear?
Is the closed cooling system loosing any anti freeze?
I think some more information is needed here.
Because you have a known good (second engine) the key to finding a problem sometimes like in your situation is to use the parts from known good engine to check and see if the engine with issues same parts have any problems and if not no need to replace.
So every part so far has not been needed to fix your issue. Lesson learned!!
Now your description is hard to understand,
since the issue started what have you done?
list everything you have done.
In any marine cooling system there are 4 major categories,
Water in (pick up, strainer, impeller, hoses, rusted ports that the hoses connect)
Temperature control (heat exchanger and thermostat)
Temperature information (sender) (gauge)(wire harness)
Water out, (elbows, manifolds if raw water cooled)
Rarely does the engine mounted water pump (circulation pump) ever fail.