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Thats a Phosphorus deficiency, you need to buy a Phosphoric fertilizer or just purchase the mixture of fertilizer NPK 3:2:3

The following link is to an article about fruit tree propagation: https://www.gardeningknowhow.com/ornamental/trees/tgen/grafting-trees-what-is-tree-grafting.htm
Unfortunately the probabilty of stems from a tree rooting is not verry good. Usually woody stock is taken at the correct time for that particular plant, prepared, dipped in the correct rooting hormone and placed in appropriate media, under mist, with bottom heat.

Experts agree, "Tree topping hurts trees". Please read this article: http://pubs.ext.vt.edu/430/430-458/430-458.html
If your vegetables are getting 6-8 hours of sun, some shade late in the day shouldn't hurt. Actually, they might appreciate the shade on hot days.

You should be able to find copper fungicide spray at a local plant nursery or a farm supply store. The impact on nearby plants should be minimal as this is a fungicide and should only affect fungus.

Basically, any type of mulch is fine, depending on your preferences. You may want to go with something natural which allows for good air flow and would break down over time, adding nutrients to the soil and roots. This article will help: https://www.gardeningknowhow.com/garden-how-to/info/whats-the-best-mulch-for-my-garden.htm As for ground covers, ivy and minor vinca are both popular choices for under tree ground covers. Here are some other suggestions: https://www.gardeningknowhow.com/special/shade/ground-covers-for-shade.htm

This article should help you figure out if your tree is dead: https://www.gardeningknowhow.com/plant-problems/environmental/how-to-tell-if-a-plant-is-dead-and-how-to-recover-an-almost-dead-plant.htm