First my apologies for taking so long to answer this. I just now found your question. The black dots are scat from a caterpillar or  green worm that is eating the leaves. Look under the leaves to find the  culprit and pick it off. Second the buds you see are the start of tomatoes and you must wait for the buds to open and the yellow flowers to fade before the fruit will form. The bottom leaves turning yellow is most likely normal as the oldest leaves will weaken once the plants grow large. You can pluck off the yellow leaves. You did mention the plants were growing large so congrats as I think you are on your way to a late summer tomato harvest. Keep growing, Marianne Binetti