Erin,
You are describing a whole lot of different issues here - object guarding, food guarding, location guarding, and several others.
I think it would be best if you consulted your trainer - IF she is a positive trainer - about all of this. Some one-on-one sessions would probably be called for!
Several times you talk about him barking and "freaking". It's hard for me to picture exactly what he's doing. When your Mom reached to pet him, he barked. Did he growl? Did he nip at her?
When other dogs try to smell him back, what does his "freaking" look like? Barking? More?
How does he act when he is "jealous" of you petting other dogs?
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