(Flow should get better over time as the sand starts to get a biological film over the grains.)
Wow that is quite the writeup for water changes.
Neat ideas!
I suppose an alternative to flow meters on the peristaltic pumps you could install high and low level sensors in the sump? If one of the pumps failed, blocked or otherwise became out of calibration it probably wouldn't take long for the sump level to rise or fall so a few float sensors in there might be a simple approach ?