Hello Panther, did you install the timer libs?
For this project you need a mega and lucky you it seem to have 6 hardware interrupts so you should be good.
Must say that I am not sure at all it will work, currently I finished my output dirver board (the 4 injector drivers and 1 PWM output for the pump pressure) but the PWM doesn't work. (the arduino does drive PWM but I made an error on the PCB)
Got my tiny automotive pump connected to an 0,75Kw motor but when making pressure it stalls (so the pump will ask for over 2HP I think) I will set it up in my lathe which should be powerfull enough.
Since the PWM doesn't work I use a car battery and some big fat resistors to control pump pressure, from the past I know that with 3V it delivers about 600bar and with the full battery load (13.8V) over 2300bar.
Also have some trouble with the injectors, they have been laying in stock for 2 years and they are jammed despite being filled with diesel. (hardware troubles it is, got one going now, will open them this weekend I suspect the diesel has turned into grease 
The arduino addon hardware I am making in Fritzing, one output board and one input board, when both finished and working I will post the files here to, OK?