I love it very creative.
A couple things. Algae may grow in the res. so you may wish to paint it as well as the pipes so light does not penetrate. For a flood and drain you will need a float switch so that when the water reaches a certain hieght it stops the pump. I like the bubbler air stone set ups. If you want to use the 2 litter bottles and have many plants you can get mini air stones 1 inch by .5 inch. http://www.petsmart.com/global/produ...=1141781853271
You are obviously intellegent and creative so you should have no problem making a system setup. Grow rocks and rock wool would work in this set up with a bit of cocofiber if you can do it for organic flavor. A mesh screen may work to keep the medium in. The sell plastic one at the hardware store. If you were to drop in net cups you could have a return on the pipes into the res and run airstones which you would have to feed the air pipe through the nute pipe but it should work and no need to secure them to anything as they will not fall thru the holes I dont think. The pump would have to maintain enough pressure to get a inch of nute mix in the 2 liter holder unless the setup you have was for a return only as well as the air tubes and you infected the nute in through the sides with a sprayer or tube depending on the pump size you wish to incoporate.

Dont let people get you down thats very creative, and as Einsten said, "Imagination is more important then knowledge"

One love
c