I'm no expert as I am learning about crate training myself with my 15 week old pup. But you mention that Pesto is in his crate at night, and then again when you leave. You haven't said how long Pesto spends in his crate per day.

Most of the stuff I have read on crate training says that aside from night time, a dog should not be in the crate for more than 4 hours, and between times there should be a minimum of 1 hour break.

My pup adores her crate. I leave her in it at night. In the morning she gets breakfast and a good walk, then she goes in her crate for a couple of hours. I go to work. My son lets her out after 2 hours, or if he is at uni, I drive home from work to let her out ( My husband and I have our own business so I am lucky as I can do that). She gets about 30 minutes in the back yard minimum for poops and pees, & play time. Then she goes into a 'puppy pen' I bought which is like a child play pen, but made of a series of 8 metal gates that I can form into a circle, square, rectangle...whatever. she is in that for max 4 hours, before someone is home, take her for a toilet break, a play or a walk, and then after that on some days its back to the pen until about 5pm - 5.30pm, but on others she gets to follow us around on a retratcable leash so she has some freeedom (though limited) and is involved in what the family does around the house. In the evening, she is on the leash close by me in the house, or she is in her pen (during the day its in the family room, during the evening its sometimes in the loungeroom. Then at night, she goes into the crate (though she is not sleeping through the night yet without getting restless...at which time I wake and take her out for a pee because I strss that she might not be able to hold it ).

So anyway, what I am trying to say is that the crate thing is really good, but I think we have to be sure not to over use it. I would look up dealing with 'separation anxiety' as well. The only other suggestion I would make is to find a dog behaviourist or a trainer....a dog whisperer...thats what we all need! I think the sooner you find a way to make it work, the better for Pesto and for you.

By the way, You're a gem for rescuing Pesto! I wish you every success in making his life a happy one for all of you to enjoy.