Glad to see photos of you pruning it. I think thinning it out to let sunlight through will help the most. All that moldy fungus thrives under dark areas where the leaves are thick.

Try adding something like gypsum to the soil to help improve drainage, and leech out salts from fertilizers. If the roots are black and rotting, there isn't much maintenance above that will help.

Hope your tree rejuvenates. It is so large and fruitful. Having too much fruit can also stress the tree a lot, opening it up for diseases. Removing excess unripe fruit is a good idea when the tree is having a weak year.

Thank you for sharing. It helps me learn what signs of disease look like if it strikes my citrus tree too.