There are a number of other projects which have dealt with measuring speed as an object passes between two points. A Forum Search will help there, with one thread I could find which will be useful being -
http://www.picaxeforum.co.uk/showthread.php?t=4863
In my code you don't have to really worry about turning the timer on and off, it's more a counter of pulses which only occur when the clock signal is routed through to the timer acting as a counter. You'd use the two timing points to make the connection and then break it, the count during that time is then used to determine the speed.
I am not sure the code will simulate well as it relies on the physical hardware of the chip which the simulator cannot emulate.