Howís he doing with confinement while boarded?
I agree to jump right back in and be patient, trust in what youíre doing with everyday training and know if might take a little longer. The good news is you are rescue people so you know all about that!
Iím not really experienced with training but Iím definitely experienced with undoing my own training mistakes
So far persistence and patience has been the answer with everything except for separation issues. The ex-pen/crating issue is concerning to me, because heís a little older, but I donít know if that technically means anything. Heís also only been home a couple of weeks and theyíve been hard weeks on everyone. Iím curious if the breeder noticed these issues and started to work on them and what might have helped. Are you in a position to call and check in with the breeder? I know our breeder was really honest with us that in the week before we picked him up, our particular puppy seemed to have a harder time with crate introduction and being left alone. She considered matching us with a different puppy but I was naive and motivated and otherwise the puppyís temperament and very quick learning were a good match for us. Plus, my son told everyone over and over again he wanted a puppy who would follow him everywhere and he definitely got it!
I personally think if thereís even a question of separation anxiety a trainer should be involved, or at least consult to observe, and your situation is even more vulnerable. Especially because if you typically travel and work and he does have separation issues youíre going to need your whole family involved in resolving this issue, and a point person can help form a plan and provide support to you.
The reason I think this is so important is most of the typical advice and training you will receive about crate training can actually make it a lot worse if there are true anxiety issues present. One example of this is ďwaiting outĒ or ignoring crying. A typical puppy will respond to this approach, but a puppy with anxiety will become more and more distressed. While typical puppy adjusts with time, the puppy with anxiety will already have his fears reinforced by the time the problem is clear and there isnít improvement.