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I think removing them and the distance they were from your plants would be adequate safety measure for your garden and plants.
Your fruit should be just fine and safe to consume.

https://www.gardeningknowhow.com/plant-problems/pests/pesticides/mothballs-in-gardens.htm

Watering issues could very well be the cause of yellowing leaves.
Check the soil instead of watering on a schedule. In hot weather you may need to water twice a day.
Make sure the container is draining well.
The soil you used contained a slow release fertilizer. Make sure you do not over fertilize, as this can burn the plants and roots.
Too high of nitrogen levels can be one of the causes of Blossom End Rot.

The links below will help you to make adjustments.

https://www.gardeningknowhow.com/edible/vegetables/tomato/growing-tomatoes-pots-containers.htm
https://www.gardeningknowhow.com/edible/vegetables/tomato/yellow-tomato-leaves.htm

https://www.gardeningknowhow.com/edible/vegetables/tomato/tomato-blossom-rot.htm

The markings on the tomato appear to be the work of some type of sucking insect.
Yellowing leaves on tomato plants can be due to several reasons, including pests.

Inspect the plants more carefully for any other signs or evidence to help you pinpoint the cause.
Most infestations can be treated with Neem Oil. Neem Oil is organic and safe for people, pets and bees.

Here are some links with more information.

https://www.gardeningknowhow.com/edible/vegetables/tomato/tomato-plant-insect-pests.htm
https://www.gardeningknowhow.com/plant-problems/pests/pesticides/neem-oil-uses.htm
https://www.gardeningknowhow.com/edible/vegetables/tomato/yellow-tomato-leaves.htm
https://www.gardeningknowhow.com/edible/vegetables/tomato/early-blight-alternaria-tomato-leaf-spots-yellow-leaves.htm

Drain the water, the containers and soil should always be free draining of water.

I agree, your plants are crowded and will most likely not grow and produce much for you if left in the growing box.
Moving them will most likely stress them and stunt them for a bit, but I think they will catch up if given more room to grow.

Make sure you have their new location ready, whether it's in the ground or a new larger pot.
Try to move them in the early cooler part of the day. Dig as much root up as possible, and be as gentle as possible.
Water the plants immediately and check every day if they need additional water.
https://www.gardeningknowhow.com/plant-problems/environmental/learn-how-to-avoid-and-repair-transplant-shock-in-plants.htm

It certainly doesn't sound like your plants are suffering from lack of water (the most common cause of tomato plant wilt) since you said you've gotten so much rain.

This leaves fungal disease or bacterial wilt as other possible causes, especially since two of your three plants are fine.

This article may help you, and also provides links to additional information about fungal diseases and wilt: https://www.gardeningknowhow.com/edible/vegetables/tomato/wilting-tomato-plants.htm