Have you read the wiki page on kill switches?
Engine kill switch - EcoModder
the idea is to kill power to the injectors while leaving everything else on. the engine and ECU will think you stalled it with the clutch. the engine keeps turning till the gas is burnt up (spark is still on) but no additional fuel is added to the cylinders. re supply power to the injectors and the car stays off as the ECU sees 0 rpm. bump to restart.