Help for Our Little Apple Tree

Back in 2007, we decided to plant an apple tree in our school courtyard.  It wasn't easy to get this idea approved.  There were lots of valid concerns.  Apples can be hard to grow organically, even for professionals (which we're not!)   With a little research though, I discovered that just about any pest or disease that affects an apple tree can be treated organically. 

There were also concerns that the abundance of fruit (we should be so lucky) rotting on the ground would attract rodents, and that the flowers would attract bees.  This may seem like a huge benefit considering the current crisis affecting honeybee populations, but for the school, and for the few children allergic to bee stings, it's a liability.

Since we have limited space, we ordered a "Three-in-one" grafted tree from a mail order nursery.  Since apple trees need to be planted near other apple trees in order to pollinate, grafting three trees together would allow three different varieties to pollinate each other within the same tree.  That's how we got away with only planting one. 

It took four years, but the tree finally developed fruit this year.   We were so excited!

However, now the apples have little worm (?) holes all over them. 

A sticky substance is coming out of the holes and rust-like fungus(?) is plaguing the leaves on one of the branches.  Most of the apples are falling off. 

I can't say that this tree has received too much attention in recent years -- it's definitely under-watered.  We've taken a wait-and-see approach, even with preventative treatments, because we want to be sure of what we're dealing with before we apply anything.

But now it's time to do something if we want to save it.  Some visiting experts from our local extension recommended that we submit an infected branch to their lab.  So that's the plan!  But I would also love suggestions from anyone who might have experience treating these kind of apple tree symptoms - preferably organically.  

Have you ever grown apples?