LOVE the shelf idea man.. there's creativity.. give your self a pat on the back.. this is what I like to see, people doing instead of complaining.
with the clear cups, you will get algae, but all I understand is it eats some of the nutes.. nothing more.. and there a bitch to scrub out more so then a normal rinse / cleaning
Those clear cups are covered with red bigger cups. So the Clear ones are 16oz and the bigger cups are 18oz. Covering them will stop any Algae and will also allow the roots to grow in the dark.
These most be little (big?) beasts by now....love this thread...!
I will update later this week. Been really busy at work so I haven't had time to do one or really deal with any of my plants.