Dear Peter,
You're surely correct in that it's probably cheaper with hardware timers. Problem is I don't have them at home right now and don't know how to go about designing such a circuit. The Arduino on the other hand is sitting on my bench and is just waiting and wanting to be used - maybe until I find myself a couple of timers and learn how to use them.
Regarding the cap, I should probably include one over the primary coil then. Does it matter greatly what capacitance? 220 u or 330u?