Oh blue :-(
I just wanted to talk you through my pup's journey over the last few weeks. He's just 16 weeks at the mo, and at 13 weeks, I was ready to give him back. He was barking at the end of his lead at every person who came anywhere near, barking in a really aggressive looking way at dogs at a distance, and hiding behind me whimpering at dogs that came close. He was increasingly starting to show other anxious behaviours: avoiding the harness and lead; growling when I picked him up.... I felt like I'd totally mucked up my socialisation, and ruined a perfectly good puppy, and went into a huge downward spiral. I don't think of myself as having anxiety (although my son does, and I suspect the traits come from me!) but I was crying all the time; going to sleep the minute dh came home, really not coping. Three weeks on, and 5 sessions with a doggy behaviouralist, and we can go on a couple of lovely walks a day at a few local parks: he sometimes barks a bit in the first few mins, but after that is happy to meet friendly looking dogs and play, or ignore them, come with me if I think they aren't his type ;-) It's been a bit like magic, but really it's just chicken and a clicker ;-)
Obviously, what you have is a different issue, and chicken isn't the solution - but I did just want to give you a sense of how far they can come really quickly at this age. We still have LOTS to work on: we are only just getting back to doing pavement walking, and I don't think he's solid near little children or runners yet (too exciting!), but I can believe we can get there now.
Can you go out for a short while this eve and do some recording so you know what you are dealing with? (We are doing this every time we leave ours at the mo, although we haven't left him long yet). I would really recommend a good behaviouralist if you have any money to throw at the problem - separation anxiety is SUCH a common thing (1 in 10 dogs apparently) so they'll have lots of good ideas to help you I'm sure.
If it helps, I gave myself a deadline: I'm going to work with him for x weeks, to try and fix this issue. If I haven't seen an improvement by then, I'll look at my options. It just helped me calm down and focus on the now, rather than going into panic mode. Well, it helped a bit anyway!
Sending lots of calming vibes for you and bluepup.