OK, thinking about it, I would add circulation pump suction of pump at exit of effluent water, here to let bacteria do its job, first, before disrupting denitrification . Flow of recirculating pump not to important,but fast enough, because it won't be introducing oxygen back at plenum. I would build a trap , where detritus can settle and remove/clean it, if need be, (I know your not planning to, but in case) where detritus settles this would be where water enters before plenum. I'm afraid if detritus in plenum, it will build up and continually change water flow through coral gravel medium. Or build taller plenum, to compensate for detritus build up. And design whole box to remove to clean it in near future. If need be. Next I'll go into controlling flow into and out of box.
Just remember, if I'm correct, for 100 gallon aquarium 2 gallons per hour good flow of effluent going back into aquarium, faster even better.
I like all the ideas! I just started a new thread under DIY for this type of controllable sand beds. Lets continue there: https://www.reef2reef.com/threads/controllable-deep-sand-beds-a-discussion-thread.424449/