Wow, haven't been around in a while, nice to see things are back in order.
As for the Dixie cups...I take either a hot soldering iron, or a drill to the cups ad make a bunch of holes in the lower half of the cups.
I fill them with Hydroton clay rocks for the medium.
Once a week I pull up the cups and clip the roots a bit to keep them from growing down into the pipes. I use the 1 liter bottles, not the 2 liter and the dixie cups seem to fit nicely.
I don't grow large stuff in my system, mostly lettuce and herbs and they don't seem to mind the root trimming at all.
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