Hi, you need the leaves for photosynthesis. Only prune the very lowest leaves. You prune the suckers growing between the main stem and lateral stems. They will produce fruit but slow down what you have right now. Also, how often are you watering and fertililizing? Tomatoes need water but don't like too much and the are heavy feeders. If you are using containers, depending on the size you might have to water at least once a day either early morning or late afternoon, and don't let the leaves get wet.

I've been pruning the lower leaves, suckers and some of the large leaves at the top (but only the ones that have been yellowing or otherwise appearing unhealthy or nibbled at), there's still lots of top leaves though. When it was extremely wilted, I over-watered it a bit, but only from the tray beneath rather than the top of the soil. It went from wilted to perky within the afternoon, so now I'm just watering (again from the dish beneath) in the morning to keep the soil just wet enough that it doesn't seize up. Leaves have been kept dry. What should I be ideally "feeding" it? I've used Miracle Gro since bringing it home but am open to other options.

I recommend Mykes organic fertilizer. You should use something for tomatoes. It should have a higher K content than N(nitrogen). I would not use Miracle Gro because you could end up with more leaves than fruit. It's okay to water in the pot as long as you do it slowly and thoroughly and making sure it doesn't sit in water. If what you're doing seems to be working then that's ok. I do container plantings and it's always a challenge to make sure they don't dry out or get over watered.