What Boizeau said. I would suggest removing the tree, particularly if it is a standard, (not on dwarfing rootstock) and buying a well-started tree from a good, reputable nursery. In two or three years you could be eating excellent fruit from it. There are excellent discussions here on the different approaches to pruning apples- vase or central leader, and so on. Your county extension agent can point you to good material too. Expect to have to control codling moth, at the very least. If fireblight is an issue you might want to consider a tree that is naturally blight resistant. I believe Empire is one; I have a Liberty that seems untroubled. Same for cedar apple rust. The connection between fireblight and pruning is two-fold. Pruning active fireblight probably can spread the bacteria, so real caution is needed; dormant pruning will stimulate new growth in the spring, and that new growth is more susceptible to infection. Good luck, Mark

Mulberry: Cherries don't get fire blight so no concern there. It might be better planted 10ft away or at least a few feet. But for us backyard growers other considerations usually prevail. So I'd say plant it wherever is best for sun etc. Do remove all of the apple stump that you can if it's rotted. But again I won't spend $$$ removing a solid stump.

Fruitnut - Thanks. Any pointers on what I'm looking for with cambium damage? What does that type of damage indicate? Applenut - I had been using my felco bypass pruners. What do you mean by little clippers, and are they less likely to spread fire blight? When using pruners, I did disinfect the pruners with lysol spray before doing the thinning. I didn't disinfect between each cut, as I had not seen evidence of fire blight. Is this a valid approach, or should I handle differently? Is the lysol spray as effective as a torch? Also... from the photos... some of the stubs that have fire blight are pretty short and lead to one of the future scaffolding branches (similarly, there is one near the top of the leader). The first photo is a good example of this. Do I need to remove these scaffolding branches (to 6-8" inside of the last fire blight)?

Fire Blight enters the plant from blossoms or wounds and the bacteria can be transferred on pruning tools. The symptoms you describe could certainly be caused by this bacteria. Here is a link to information from the University of California at Davis which gives symptoms and treatment options. Here is a link that might be useful: Fire Blight