My boy was crate-trained before he came to me. His issue was not being crated, it was being alone, crated or roaming free. He was/is fine in a crate as long as somebody/somedog is with him (not in the same crate, just around). He exhibits SA issues if he's crated/roaming alone. He is much better now than when I got him four years ago. He still has mild SA issues, which we manage by giving him access to an indoor/outdoor kennel which my husband built which gives him room to run around and release his anxiety. I also give him a filled, frozen kong for distraction purposes.
What we do now to manage his mild but lingering SA issues is a far cry from what we did at first…we tried everything and anything. We also had a wonderful woman giving us SA advice.
I suggest you give him some time, and if he doesn't settle down, bit by bit, slowly but surely, you'll need to look into alleviating/managing SA. SA is not an easy issue to deal with, it takes a LOT of time and patience to discover what works best for your pup...there is, unfortunately, no one magic bullet. I wish you the best of luck with Jacob, designcrush72. Don't give up, it CAN get better!