We brought our 13 weeks old Basenji, Omar, home last Saturday, and are struggling to train him to spend any time alone. We are crate training him, and are currently also litter training him (he still has pee accidents when he gets too excited/distracted, etc, but considering it’s only been a week, I think he’s made good progress in that regard!).
He is refusing to learn (or acknowledge he knows) how to “go to bed” in his crate, but the last two nights he actually put himself to bed in there when he got tired, and slept through the night with only one request for a pee break, which has been a very welcome breakthrough!
If he is in his crate in a well trafficked area and he knows one of us is around, he’s generally ok to stay in his crate for short periods of time during the day, but as soon as we leave the room, he goes full banshee mode. We are not acknowledging him when he does that, and not opening his crate until he is quiet again. Because my husband and I both work, there are some days when he does need to be alone for 4-5 hours. We have set up an xpen that fits his crate, litter box, and a small play area, so that he will be able to eliminate outside of his crate when we are not home for longer periods of time, but he starts his screaming in there, too.
We have been doing the “leave for short periods of time then extend them” training but he seems unaffected—if we are gone or out of sight, he’s going to scream (whether he is in his pen or the crate). I suspect, when he was left alone for 3 hours yesterday, he screamed the whole time. 
We have been playing with him in the pen so that it’s a “fun” place, and tried only giving him a special treat when he’s in there (Kong toy, etc), but at most this keeps him occupied for 5 minutes before it’s abandoned.
I don’t know if he will eventually get used to being alone and we just need to keep at it (like we did with him being crated at night) , but I’m concerned that, rather than him learning we always come back, he will start hating going into the xpen specifically, because that’s where he will be when we are gone for longer.
Any suggestions you have for an approach/solution would be fantastic!
@rhapsodomancy - If I am reading this right, why when you are home is he confined and not with you other then bed time? He should be with you when you are home
Separation anxiety is sad and difficult. (1) You might consider getting a companion - even temporarily. It could help teach him how to handle being alone. (2) A tired dog is a good dog - is he really getting enough exercise? If he is exhausted when you leave, it could set a new pattern of sleeping when you're gone. (3) When you are home, you might keep him on an "umbilical cord" to keep him safe and in sight (this also helps with potty training). A very light chain leash will keep puppy teeth from chewing through an annoying tether (or soak a leash in bitter apple).
I hope this is helpful.
Thanks for the suggestions, Pawla—we are trying to get in as much activity as possible before we leave him (long walk plus playtime). He’s usually ready to pass out at that point, so I’m hopeful that as his familiarity with the xpen and his surroundings grow, so too will his ability to give in to his tiredness, even if we aren’t there. We have two cats that he is trying desperately to befriend....they aren’t particularly enthused yet, but fingers crossed. At this point an additional dog companion probably isn’t a possibility. Right now he has free rein of the downstairs living/kitchen area when we are there (we’ve got baby gates at both staircases). We may try the leash suggestion when we are upstairs, as otherwise one of us is bound to that area, too, unless we are prepared for him to scream until we come back down (and we’re not yet comfortable leaving him with free rein unsupervised). yes the chewing the leash when we’ve kept him tethered to us is an issue so we’ll definitely try the bitter apple technique or look into a chain one (though I suspect he’d try to chew that too—haven’t found anything he won’t chew yet!)
Hi Tanya— I think you’re referring to my comment about him being in his crate in a well trafficked area during the day—that was mainly when we were working to get him more comfortable with the crate in general, which appears to have worked. He is not confined when one of us is home, except for the occasional brief period for safety, (I.e only one of us is home and needs to leave the main living area temporarily/ people are coming and going through the front door, etc).
It must be very distressing to hear your b cry. We had a similar situation with our boy. He would cry piteously when left and our girl would chime in as if to sooth him. We found crating them (their safe place) with a treat, kind words and a covering as if they were being tucked in at night did the trick when home alone. Crating occurred after a walk so they were comfortable and, as far as I can tell, they slept until we got home. Then greetings and another walk. We’ve also found letting them loose whenever we’re at home is a necessary complement to this - they are such loyal little pack animals! Have you discussed this situation with your vet? As a last resort, a pharmacological intervention may be a short term possibility during an adjustment period.
Have you tried a petcam? You could watch what he's doing on your phone and see if he settles down after a while. It's possible he quietens down and naps when he knows you're gone and starts crying again when he hears you returning. You can find monitors that allow you to talk to your boy or dispense treats, but the basic ones do the job!
