Luckily you saved most of the water otherwise this would be an expensive grow for you. Now you will need to calculate how much of that saved
nutrient solution you’ll need to add every week or 2. Hopefully the mistake hasn’t caused any damage.
The brownish marks on the bottom of the tomatoes is called blossom end rot. My guess the tomatoes that have it were the ones that were already on the plant when you were still using miracle grow. Do you see any on newer tomatoes using the new
nutrients? If yes you will need to add a little lime to the reservoir so any new tomato growth will not have blossom end rot. This video not the most exciting video but it explains why blossom end rot happens. It also shows you how to make a solution (wear a mask) to stop it from happening to other tomatoes. Add a gallon of the solution to the 55 gallon barrel just one time if you see those brown spots on other tomatoes.
https://www.youtube.com/watch?v=6uObcfRWdK0
The other tomato with what looks like a crater is called catfacing. It can be caused by temp changes also by excessive nitrogen levels. My guess in your case temp changes. Those tomatoes can still be grown and eaten. You will probably have to cut the bottoms off when they have ripened then eat the rest. I’ve had some of them on my plants I wouldn’t worry much about them. Just don’t over ripen them cause they might split.