What you're trying to do is a great idea, but the computer in the Vortech's isn't flexible enough to do that.
For a completely different reason than that (but to also solve that problem), I'd consider switching your pumps to match your new tank. The mp40's yo have now have a good 24" reach, but beyond that range they are pretty weak. Running them full-bore (and clearing out your sand bed they way you did) is kinda the only way around this.
Consider switching to a pump that's oriented to flowing a long tank – you'll be able to keep more of that flow up off the sand.
Tunze's Streams are the classic choice....a pair of 6105's in there would be like the difference between night and day – much stronger than that mp40's. This gives you a lot more flow options. Gyres are probably a better choice than the Vortech's too, but they seem a little finicky on cleaning to me and not quite as flexible in use as the Stream design.
Going back to the flow plan you described...
You don't even want controllable pumps for this type of flow setup....just plain AC-powered ON/OFF pumps like the Tunze 6065, 6085 and 6125 or the smaller nanostream models, the 6015, 6025, and 6045.
All you need for "control" is two appliance timers or equivalent to turn the first pump ON for a few hours while the second pump is OFF.
Then, a few hours later the timers turn the first pump OFF and the second pump ON for a few hours.
This slowly alternating flow gives a great tidal effect....coals love it and it's easy to set up in most cases. A pair of those 6085's is only $320 too!