Reducing the engine compartment temperature is always good (for the alternator for example), but I doubt if the temperature rises to 100C.
It rises to 100C over the sensor, which is probably enclosed within the Sterling equipment on the power component heatsink and is meant to protect them. When it reaches 100C this means that the internals of the power components are close to their limit (typically 120-150C). However this could also happen at say 60C when there is not enough air circulation over the heatsinks.
Until you solve the air circulation of the whole compartment, if the unit is not already equipped with one, you could try adding a small fan which blows directly over the heatsinks - there is a drastic difference in heat dissipation when comparing forced air to natural convection.
I have a 2004/B36, which I assume is very similar, and I really do not see the proper way to create circulation, since proper circulation requires the air to flow by (i.e - one way). The engine compartment is open towards the lazarette and the air intake port is under the helmsman seat. So creating a flow means pushing it into the saloon - not desirable.
Maybe it is possible to change the flow direction by making an opening below the steps and using a fan to force the flow backwards - not sure how well this will work.
Or, maybe it is possible to spread a flexible duct (like those used for HVAC systems) from the front of the engine compartment, all the way back to the transom and fit over there a fan with flapped port -not sure how good this will behave in following seas.
As said - don't really see the proper solution.