Looks like you might not have pruned the tree enough if you pruned it at all at planting time. When trees are transplanted they lose like 90% of the original roots from the nursery, so the tree needs to be cut back to 3-4 feet in height and the branches all cut way back near the trunk. This will restore balance between the roots and the rest of the tree. Otherwise the root system just isn't good enough to support the size of the tree you have there. So it makes sense that if the root system is small, the tree isn't getting enough water or nutrients to keep it happy. I would basically chop the tree in half and it will do much better. Seriously.

Totally normal. Don't fertilize and don't cover it. Cut watering back to once every 2-3 weeks. If it where an older tree that had been in the ground for a few years you would be cutting the watering back even more than that. Just leave it alone and let nature take its course.

Yes, the pot looks small and the plant looks underfed. You are giving it only about a quarter of its nutrient needs: Citrus Focus instructions say "Add 10ml of Citrus Focus in every litre of clean water, weekly. If leaves are pale or yellow, increase frequency of application."

Thanks for asking. It doesn't seem any better, but it doesn't seem any worse, either. I gave it a good soak and looked for signs of insects or mold. But I haven't called the county extension office. Treebarb, its two types of apple trees that are twisted around each other. gjcore, thanks for the book recommendation. I've lived in homes with mature fruit trees before, but I've never grown them from saplings before.