Do you need a hardware or a software timer? How precise should it be? If a software timer is sufficient, than you could use "tick counts". So, read both channels, wait for a change in channel 0. If a change is detected, get the current time with "tick count" and store it. Detect and wait for the change in channel one and get another tick count. Substract both and you have got your time difference in msec. Of cause, thats not too precise, just as good as the speed of your HW/SW.
