Slight regression back to the mechanical side of life. I may have missed how you auto rinse and remove liquids from the cups.
To clean the cup, I use the same type of peristaltic pumps that I am using for everything else.
For rinsing I just pump RO water into the cup.
For the drain I have a tube that runs down to the bottom of the cup. There is a pipet tip on the end of the tube that touches the bottom of the cup. Thanks to water's tendency to stick together it pretty much gets 100% of the water out. I drain, rinse, drain, and repeat 3 times so if there is any water not removed it should be almost pure RO water. And pure RO water in any quantity has no impact on the results.
You can see the drain line in the photos - it is ziptied to the pH probe to hold it in place.

