Growing in self watering containers is different from growing in the ground, where it's best to rotate your crops, especially the ones from the night shade family. That's largely because of soil borne diseases like verticillium and fusarium wilt build up over time. I am new to self watering containers, but I've been frequenting the Earthbox forum and followed the activities of Raybo, who invented the Earthtainer. They recommend removing the old plants with their rootballs and about 20-30 percent of the old potting mix. Then they mix in the new mix along with a full dose of lime and fertilizers as you did the first year. You can do this for a couple of years so long as your mix doesn't get compacted and your plants stay disease free.

Soil pH is a measure of the "potential Hydrogen" in the soil. In soils with low pH there are more free hydrogen ions while in soils with a high pH there are few. If you need to decrease the number of hydrogen ions Calcium Carbonate (CaCo3, lime) has been found to be the best way to do that while adding sulfur will increase the number of hydrogen ion. Rain water typically is acidic and has, over time, lowered the pH of some soils and some bodies of water. Most all municipal water systems add, in addition to Chloramine and Floride, something to make that water close to neutral since water very acidic or alkaline simply does not taste good. Adding Gypsum to soils that are not sodic is usually a waste of time.

I have friends who use the SqFt system and enjoy it a lot. Saves on tilling and or re-working the soil as no one steps on that ground. I love the buttercrunch head lettuce, it doesn't taste like what they try to pass off as butter crunch lettuce in the stores. All greens, lettuce, cole plants carrots onions, herbs, turnips, beets, redishes, Strawberries. Some love the system some don't I sure hope you left or had none or not much damage. We came out very well on the west side, only lost power for a day.

If seedlings are close together, I would snip the ones I don't want. However, yours are far enough apart that pulling one won't disrupt the others. There are some City Picker container types that are sold with a trellis. Since you didn't get that one, you will have to set it where you can have some trellis nearby. For example, put it near the edge of patio or sidewalk somewhere. The trellis vertical shafts will be in the ground and you buy netting or make your own. You can also do the same on a patio or cemented area if you put the vertical shafts in a container of cement to hold them down. In this case you mentioned you have a deck. Using the deck's horizontal structure, along with additional support for the vines, will be a great way to decorate the deck as the plants get bigger. I think the current plants are fine but definitely there is a reason that many container varieties exist. However, with your deck, it sounds like you won't be lacking for horizontal space, and you can make vertical space, so I think you can be OK with keeping what you have.