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There is not much you can do except keep an eye on them. You may want to pre-treat the soil with fungicide to help keep root rot from setting in.

If you are having issues with drainage now, even if it is due to heavy rains, this indicates that you may want to amend the soil to improve the drainage.

These articles should helps with that: https://www.gardeningknowhow.com/plant-problems/pests/keeping-ants-of-flowering-vines-vegetables-and-flowers.htm
https://www.gardeningknowhow.com/plant-problems/pests/insects/get-rid-of-ants.htm

Thuricide can be sprayed on any plant, vegetable or fruit without posing a hazard. Bacillus thuringiensis (Bt) is another option. Since this is a selective insecticide, it kills tent caterpillars while remaining safe to humans. Here is an article that you may find helpful: https://www.gardeningknowhow.com/problems/pests/tent-worms-tent-caterpillar-home-remedy.htm

This is most likely lichen, and a symptom that the tree may be ill, as lichen usually like to attach to trees that are unhealthy. This article will explain more about lichen: https://www.gardeningknowhow.com/ornamental/fungus-lichen/treatment-tree-lichen.htm

Without knowing what fruit it is, I would suspect that it is black rot or brown rot. This article will help:
https://www.gardeningknowhow.com/edible/fruits/peach/brown-rot-fungus.htm

It sounds like leaf galls, which are unsightly but harmless. There is not much you can do about them. This article has more information:
http://gardening.about.com/od/insectpestid/qt/LeafGall.htm