If you're like me and hate hate hate bird netting, you might want to try tulle fabric. It's inexpensive, very light, and excludes all but the smallest insects (as well as birds). It's not as durable, though, so you have to handle it with a bit more care. As for the repotting question, if you're merely transplanting and not excessively disturbing the roots, you could probably get away with repotting any time of year. Ideally, though, you'd go a step beyond and completely refresh the potting mix (i.e. bare root the plant), and that's best done in late winter/early spring before it emerges from dormancy.

I've grown squash in 5" net pots inside a 6" pvc pipe and tomatoes, peppers and eggplant in the 10" net pots inside 3 gallon buckets. Both ran drip for a few minutes each hour, not constant like nft so I needed more medium. The net pots had grodan and clay pellets. For things in nft or water culture I would use much smaller since the roots grow out the net pot more. For drip and ebb and flow a little bigger is better to hold the moisture. The medium you use makes a big difference too, rock wool holds way more moisture than perlite or clay. There is no set guidelines I've seen but the plant will let you know if it needs a bigger pot.

Thanks Blue. I can now see you are 100% right - the 18 slice 2" mesh net pots came the other day. They weigh 4.0 grams each, too flexible, and the lips are tiny and molding shoddy. The only way to deal with them would be to buy a 1 7/8" hole saw. To add further insult, about 10% of the lips were not completely molded, i.e., missing material and are worthless. These disappointing mesh net pots came from hydroponicsnation in CO via eBay. They are obviously not reliable for most veggies, though they might be pretty good for Spiritweed, garden Dandelion varieties and the like. I may just snip the 16-slice bottoms out and insert them in the durable 4 slice bottoms I'm using currently when I get a chance. They came from homeandgardensupply in RI via Amazon, and weigh 4.5 grams, which made all the difference to their integrity and clearly superior durability and molding.

The 3.75'' would work for tomatoes because I currently use them for my DWC system. What kind of plants are you planning on growing other than tomatoes? To be honest, given the area of 11'' X 11''you are talking about I would bet you could fit one, maybe 2 toms at most in there... now I could be wrong... do you have any pics? that might help. Tomatoe roots get very large and will take up TONS of space in your setup. From what I understand you are using an Ebb and Flow "tray" method where the tray floods and drains. How deep is the tray? Do you have any pictures?