I have got the last code posted to work with a few changes; I have put the hardwareCounterPin back on 47 and changed the Timer from 4 to Timer5 and edited the Servo library.
The previous Counter sketch would not work as both the counter and the servo were using Timer5. MEGA 2560 has three 16bit timers but only Timer5 has an event capture pin which the counter needs to pick up the anemometer pulses. The servo library automatically selects Timer5 so I have removed it from the Servo library and now the sketch works.
The original RPM code would not work as the loop() delays were affecting the interrupts; they are not compatible.
Next step is to put the Anemometer outside and connect to it with zigbee or ethernet; as the servo and counter sketch will be on different boards there will not be an issue with timers.
Thanks to Nick Gammon and johnwasser for their help.