When looking at the raw water circuit (and yes it is a circuit just like electricity) the flow is equated to the current and is fixed based on overall resistance (tube size, length and number of bends in the circuit) and the pressure (function of depth below waterline and characteristics of the raw water pump.)

In my humble opinion there is no need to measure flow at the pump and at the exhaust. It will be the same provided that there are no known leaks in the circuit.

Since you have changed the resistance quantity (removed the vented loop – reduced pipe length and # of bends) and the temp alarm did not sound then you now can assume that you can solve the problem in one of 2 ways.

First is to change the resistance characteristics of the raw water circuit while including the vented loop. That can be done by increasing the size of the pipes used (external to the engine) and the number of bends and their angle (use larger radius for the bend and less then 90 degree angle). At this point for a given (old pump) with same pressure as before will result in increased water flow.

Second is to change the pump for one with increased pressure. Given that the resistance is the same. This will result in an increased flow which will cool the fresh water to a lower temp and solve the high temp alarm.

There is another potential solution which depends on preference. It is more radical approach as it does not bring the engine to the designer point of work but rather changes things.

In some engines (my own Perkins 6345 114HP) there is a cooling function of the transmission that is done on the engine cooler. On my engine the raw water first cools the engine oil then flows to the transmission cooler and lastly goes to the fresh water heat converter and finally injected into the exhaust to be output overboard.

There are 2 options here:
First to add a dedicated transmission cooler with it’s own pump and heat exchanger. That will reduce the temp of the transmission oil and will require less calories to be absorbed by the raw water circuit of the engine leaving the potential to absorb calories from the fresh water heat exchanger.

Second is even more extreme: add another external heat exchanger for the fresh water circuit which is powered by another electrical raw water pump and can be activated when needed (over-temp alarm situation).

To sum things up: Best is when there are no problems and restoring the engine to the “like new” operation by just cleaning (flushing) the system, removing resistance and restoring pump functionality. Second is when first choice does not work, then some radical solutions are needed and chosen based on owner understanding and desires.

“Luck favors the prepared mind”

Efraim SV Aliza