Nucky,
I am so sorry you and yours are going through this.
Beagles are known to be among the most laid back of breeds, but it sounds like your guy has been through a lot. As we know -- just like with humans -- Nature/Nurture -- both have an effect.
I found an article for you on the ASPCA website. It goes into detail, not only on how to deal with separation anxiety, but also talks about what could be the causes.
(There is a play "Sylvia" that is about a dog that was a rescued stray. Sylvia is a dog played by an actress. I love this play and have seen it 3 times. There is a line that Sylvia says to the man who rescued her:
Sylvia says, "There are some things about me you will just never know."
I have always remembered that line and could picture our dog Annie saying it. Annie arrived at our back door and we took her in. She was with us for almost 17 years. But we never knew anything about where she was before that long-ago, April evening, under a full moon, when she looked in at me through a screen door.
I thought about naming her Moondoggie, but we went with Annie because she was an orphan before she found us.)
But I digress. (blush)
Soooo anyway, here is a good article that I hope helps:
Separation Anxiety | ASPCA