Please forgive me in advance, but I've got a question.
First, though, I should say that I recently retired from the SC DNR, where I worked at the Marine Resources Research Institute here on James Island.
Over the years we had many different fresh and salt water aquaria, from as small as a petri dish up to tens of thousands of gallons (large animal, brood stock and grow out holding tanks).
One in particular, a seawater coral reef (100 gal) on public display, was probably the most difficult to maintain (coral being more than extremely picky about their environmental conditions).
In all these cases, except where we were simulating 24 hr tidal flow conditions, the water circulation was kept at a constant rate, 24/7/365.
So, my question is: Why are you needing to pulse your pumps?