The 2-litres should be just fine. What you're describing is known as a Sea Of Green (SOG). Basically it just means you grow many freshly-rooted (1-2 weeks) clones packed together as tight as possible to produce X number of large colas. The lower branches which yield only popcorn nugs are often pruned after the first week or two of flower.

Sounds like a cool idea. Just make sure you light-proof the bottles so light doesn't get to the roots. :thumbsup: