Separation Anxiety?

I'm new here and in need of some advice, it sounds like other people here have dealt with similar issues.

A month ago I brought home a terrier mix Pete from a rescue. He is not only adorable (looks like a little fox!) but has a great temperament, gentle and very loving. He's been socialized in a lot of situations and acted like a champ, friendly with dogs but not super interested, really a people dog.... maybe a little too much so.

He had been at the rescue for a few months and we were told he was crate trained so we set one up in our kitchen thinking it would be a nice haven for him in an unusual environment. The first day he was literally on our (especially my) heels all day. He walked right into the crate and lay there for a few minutes in the afternoon. When evening came I sent him in there and went upstairs to bed. He proceeded to SCREAM and intermittently claw at the door for 3.5 hours with no break. I know you cant let them out when they're frantic but by midnight I was desperate and clearly he was too. I went downstairs and sat for half an hour till he fell asleep, I thought I could sneak away but as soon as I moved he was awake like a lighting bolt and I decided to take advantage of the lull to let him out instead of letting him get going again. He whines when he cant see me for a moment and refuses to go outside alone.

I'm home most of the day but I had a few appointments that required me to be out for 3 hours at a time, I'm pretty certain he barked the whole time and I came home to a puddle of drool. Another time we left him in the house with my brother (who got locked in the bathroom for an hour... hilarious) and when we came home Pete was barking at the door and had COVERED our front hall with sweaty pawprints, not one or two trails but layers of solid pattern. I have done LOTS of research and have been trying to get him used to being alone... all the standard stuff, no intense greetings or goodbyes, desensitizing him to triggers like opening the door, leaving for a few seconds then a few minutes. He still whines but wont start barking until about the 20 min mark.

He doesnt seem to destroy things or soil the house *thank god* but I can't spend my whole life inside my house... I've been assuming its SA but we're at the 5 week mark and have seen only minor improvements. I really want to fix the problem and make darn sure I don't make things worse. Advice? Suggestions?

Any help or support would be appreciated.