Engine heating
 

I assume that the exhaust comes out the prop. So you can't check the water flow out the exhaust.
when is the last time the seawater pump was serviced with a new impeller.
The other thing do it yourselfers forget is to clean the passages and check for blockages on the intake side of the oil cooler.
Pieces of the impeller tend to find their way into the oil cooler.

Wouldn't that be a fwc engine ? Presuming that it is have you cleaned and acid dipped the heat exchanger recently ? It's very common for people to overlook the fact that they get grunged up and loose a lot of their heat transfer capability .

You say that you have a high prop height. How far below the hull is the prop shaft.
Is this a standard Bravo drive or one with low water pick up?
If it is a low water pick up hopefully it is not a dual water pick up.
Not a safe idea but set up a camera or have someone look over the back to make sure water is still coming out of the exhaust at above 3200 RPM

Engine heating
 

Maybe we should get back to ( a few ) basics.
A diesel with a B1 is a little on the unusual side. What make and model of boat is this ?
Is it new and you're the first owner and it's never done this before and has just suddenly started doing this or is it 2nd hand / used and you have discovered this problem as a new owner of the boat ?

Engine heating
 

Google search shows that to be a very sporty boat. Is it Italian made ?
Do you have any idea what the original drive system was ? If you believe that the current drive is too high is it a possibility that the old power plant had a unit that was deeper than the B1x and they utilized the original transom cutout ?
It's not difficult to confirm your suspicions that the drive is too high . Just haul the boat and eyeball the keel line in relation to where the water pickups on the drive are. If they are higher than the line of the keel then that could well be the problem .

Edit to add : If the water pickups are below the keel line then maybe it's a possibility that the raw water pump on the engine wants more water than the B1x pickups can provide and you might have to go with a separate transom mounted pickup . I wouldn't be quick to mess with the drive with spacers yet !

I have two of those engines in my boat, you can install a water pressure gauge in the big grey nut on the top of the intercooler where the sea water comes in, next to the zinc, should be 15 psi or so when running. That will tell you right away if it is a pressure issue. I have never had any cooling issues with mine but my seawater pickups are on the hull.