Answer: Rust affects the foliage, so what you are describing on your crabapple tree is something other than rust. You might look carefully and see if there is a point of entry caused by a borer or other evidence of damage to the bark.
Rust uses juniper as an alternate host, so removing the hjuniper was probably a good idea. However, some crabapple varieties are more disease resistant than others so you may wish to consider preventive spraying. Consult with your local County Extension to determine the best spray regime (and timing) for your local area. They should also be able to help diagnose the trunk problem and suggest any possible remedies for that as well.
In the meantime, it is important to help the tree stay healthy by ensuring it has adequate water and fertility.
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