If their wilting, they are not getting enough water... Try watering more frequently.

Too much rain or over-watering, which in a container that small would be easy to do. Other possible causes are lack of nutrients - primarily nitrogen. You must feed them regularly. Or being root bound in the pot. That is a big plant for that size container so it could easily be rootbound. Every time you water a plant in a container the nutrients leach out so they must be replaced regularly. When the size of the container is proportional to the plant you don't have that much of an issue. Dave

I've already removed the dead branches but you can see one hanging on the left side there and the beginnings of the next branch up. I thought maybe it was a fungal infection and sprayed with copper solution. The base/stem is starting to get fuzzy and white?

When tomato plants start to blossom lower leaves and branches will typically die off since most of the energy is being used for going into the fruiting stage. This is normal. Just cut them off. I usually cut off all lower branches up to the first cluster of tomatoes so energy is not wasted on non fruiting growth. You can also prune any new growth to force energy to existing growth and into fruit production. I see some of that on your plants but that's not what the spotting appears to be. That looks like powdery mildew from the images, hard to tell since I can't zoom in a lot, which makes sense since you stated it's been wet where you're located. Use a fungicide to knock that out or it'll spread. Increasing airflow can help as well, if possible, to help dry out the leaves before mildew starts forming. As far as your nute and water issues, it could be several things. I've run tomato plants higher than 3.5 before with no issues but it depends on the variety. Some are more salt tolerant than others. Only drinking 4 gal in 3 weeks for 4 plants is concerning. My larger tomato plants would drink about a gallon to 1.5 gal a day! You should be having way more water consumption and with very little water usage and a slightly rising EC you plants aren't using much nutes either. While your EC may be fine that doesn't mean you don't have salt buildup in your media which is common with your setup so you're adding salts on top of salts. Have you measured the EC of the runoff? What type of "drainage stones" did you use? Pea gravel and the like can really mess up your pH. You're correct that your pH can rise due to the type of elements being used by the plants but it shouldn't being rising nearly as much as yours is especially using RO water. Test the pH of some RO water and put some media in it, let it sit for a day and test it again. See if pH rises. With very little water and nute consumption it could suggest root rot issues but pH usually drops like a rock with that due to all the dead decaying matter but yours is rising so your roots are probably fine. I would flush the system with a salt remover to get rid of any accumulated salts in the media. Flush it until you get a very very low EC from the runoff. Start fresh with with about 1.5 EC. Even varieties that are less salt tolerant can handle 1.5 no problem. That's my first thoughts.