I would reconfigure so the drain flow goes back out the thru-hull intake. Ive tried about every check valve out there, including the same ones wakemakers sells, with less then ideal results. Over time, the flapper check-valves end up with a case of "muscle memory" and stay open. This will allow for the air to be drawn through them in the same manor you are experiencing with your current one.
The sac should still retain the vent line w/check-valve, so you have an audible and visual indicator that the sac is full. For draining, you can hear a change in the pumps sound when the last of the water is drawn from the sac. After a couple of cycles, you get a feel for how long they take to drain, so no need for timers.