The grind is going to fun to figure out, from what I can see the finer the grind the better the efficiency BUT what good is it if you can't separate it? I did a 4 step mash so that helped out a bunch but switching to malted grains will help.
For the first portion of the malting process I am thinking of a flooding system, a vessel of some sorts (5g bucket) with a small holes (not too many but enough to empty the vessel in under 5 minutes) in the bottom that will be flooded from a sump. An overflow switch or screened overflow will be installed at the top to ensure proper coverage of water. Once the flooding time has been meet the pump will be killed and water will slowly drain from the bottom allowing the grains to be exposed. When the rest period is over the pump is turned on and continues for another cycle.
This will be a closed loop system keeping critters out and on the return to the sump water will pass though a coarse filter and possibly a layer a carbon. Once rehydration is achieved for the grain its ready to move to unit #2 for sprouting.