Ugh, yes, sounds familiar.
We got Oji at 12 weeks, if I recall. He is now just turning 5 years old.
That first night, I realized I could not even walk out of his sight without him crying. Walk out the front door to take the trash out or something? Forget about it. Worst part: There is no place in our house that his noise cannot be heard. My wife and daughter needed to sleep. I was forced to sleep on the dining room floor – had him a few feet away from me on a blanket, but he right away came over and laid against me.
Crating Oji? He would pee every time in the crate. Most times he would also poo in there (and get all in it).
He is near impossible to board on the rare occasions I must travel.
A few months ago, we reached the point where he could be left in the house – uncrated! I began to wonder if he would have been better off all along not being crated. Well, one day we left him in the house and my wife and I took daughter to a play date and then went out for lunch. Well, it was a rainy day, including lightning. We came home to the bathroom rug shredded and pee all over that floor. After that, I did go ahead and trust him in the house loose when we were gone (no rain). We came home to find he had peed all over the front door rug.
So that is gone. He cannot be trusted in the house loose when we leave anymore.
Not to make this about me and Oji.
I guess my message is that if your dog has separation anxiety, it's my opinion that it will be with him for life. I wish I had a better message for you. Maybe I'm wrong.
Really, consider this please: He may not have separation anxiety! It may just be typical puppy problems!