Sick apple tree Need help

I have a 3-4 year grafted apple tree that was given to me last fall. I planted it where an old oak had fallen before I purchased the house. Both the main trunks have dark black spots on them. The tree still has leaves and its sprouting new branches but only from closer to the ground. There were also these little black bugs in there at one point but I think I killed them all.  I have two other apples trees that dont have any issues. I have tried some organic fungus spray but really dont know if thats the problem or if its working. Does anyone have any ideas?

Thank You

Can the dark black spots be rubbed off with your finger?  That would kind of point to a fungus like sooty mold or something.  

I have two mandarin trees that had sooty mold issues and scale for a few years.  I finally rubbed every single branch and leaf down with a rag soaked in a mix of antifungal and horticultural oil,
they seem much better this year.

As for it only sprouting branches from lower- do the upper branches appear dead or still alive (scratch bark to see if still green underneath)

Knowing a few more details, maybe even pics would be helpful.

I tried to rub it off but didn't seem to do anything. Hope the pictures help. The tree is still alive but not thriving at all.

Can anyone help with this?

Optimizing the soil's pH for what the apple trees like may help. Perhaps mulching with multiple sources and types of mulch could help, this is like when we eat off the floor, humans diversify their viral load and become more immune to sickness. Tree paste or compost tea could help as similar horticultural oil alternatives, and innoculating the trees with mycorrhzal fungi would help too.

It could be black rot, and because it is at the trunk this could be pretty tough to help treat. I would try to match more symptoms of black rot, and then apply a fungicide like liquid copper.

That appears to be fire blight infecting the trunk, at this stage you will need to use a multi level approach.
First thing to do is rake up and destroy all leaves on the ground.
Next you want a really good aerated compost tea to spray over the entire tree and around the trunk to get any spores laying in the grass and on the soil.
The third thing to do is use a compost that is calcium rich along with mycorrhizae so the tree can build defenses against a recurrence or continuation of the infection.

Erwinia amylovora is the bacterium that is causing the problem, in case you want to do some reading up on it.

Redhawk