Holy Toledo! (Sorry, had to!)
Howdy from Atlanta.
I had that problem with tomatoes we grew in earthtainers (quasi-hydro?) outdoors; they were just too close together. You should space your plants out more if you grow them outside again. While square foot gardening might work for their soil requirements, spacing them so close in soil invites fungus. Alternatively, you could prune them to thin them out and allow more air flow.
Would love to see the results of your efforts cloning and growing!