Answer: You can certainly try transplanting if they are still quite small. Another possibility is to pregerminate some seeds on a damp paper towel (enclose it in plastic wrap and set it in a warm, bright loction but out of direct sun so it doesn't overheat) and then plant them where you need replacements.
Pruning tomatoes is a matter of personal preference and there are as many answers to that question as there are tomato growers. In general, in my experience pruning is better done later in the season when you want to force the plant's energy toward forming and ripening the last of the fruit before frost, or if the plants are just out of control as can happen on some of the larger types. Some varieties also respond better to it than others. I find that the extra foliage helps to shade the tomatoes and prevent sunscald during hot summer weather. You might want to experiment with a few plants and see how it works for you.
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