Personally I think you may be getting more complicated than needed. A simple flow meter like Dywer makes giving you a per hour rating is all you really need. If your water maker is only producing 3gph you'd be better off with a simple kitchen timer set for the amount of hours you want to make water. 3 is an easy number to quickly multiply in your head
times the hours run. Most people who have non-electronic water makers do this all the time. Trying to figure out to the gallon what you need, what your water maker is making, how much water you have used and how much you want to make will be something you'll get tierd of doing. You''ll get a feel for how long you'll run your water maker to meet your usual needs by instict soon enough.