Ok, I have it sorted. Two systems required. First is the duty cycle switch system which will switch an output if a duty cycle goes above a set value. This would be set to 1% and then the output reversed (so 1 is 0 and 0 is 1). Therefore when the duty cycle drops below 1% then the alternator is energised. The reversing of the output could be simply done with a small relay.
Secondly there would be a voltage controller switch that cuts the alternator back in at a set voltage (say 11.5v) and then switches it off again at another value (say 12.5v).
These circuits are available here
http://www.autospeed.com/shop/category_579/browse.html
Item numbers KC5375 & KC5377