You'll only overheat the engine if you have an engine coolant leak; however, your time in WEP is limited. For airplanes that have WEP (most of them do) you're typically limited to about 5 minutes although some (German) are longer. Check out the coolant guage and you'll see your normal operating range is in the yellow. Once it reaches the red you loose WEP but the engine will operate normally at full power and after some time you regain some WEP time as the engine cools below the red zone.
You can adjust your prop RPM for best range and to reduce drag when the engine is windmilling but makes no difference for engine temps.
No, you can't control the speed of the ships.