I, at least, do not understand what you are talking about, your first post states you want to measure the time from one input goes low till another input goes low, now you state that you want to measure the time a switch stay open (= 1 input). In either case one issue will be raised: what else do you expect the uC to do at the same time (poll vs interrupt).
Cut to one specific problem and restate so we may help you.
Erik