Thought I'd give an update on the surviving plants. My jalapeno pepper is doing great and has a peppers all over it. I ate one the other day and it was delicious! No signs of disease at all and I didn't change my care routine so I now know that I wasn't killing it or my other plants that were sick.
My tomato plant obviously has spotted wilt but has show some resistance to the disease and has managed to power through it unlike the last one that was completely wiped out by the spotted wilt. The growth has been stunted, as well as fruit production but I've managed to harvest a few dozen tomatoes already with many more on the way! I'm glad that I only culled two of my plants and gave these ones a chance.