@eeeefarm:
You might want to experiment with leaving him for a few minutes, then a few more minutes, then half an hour, etc. to see how he manages. Do you plan to crate him or confine him in a room when you are gone? I find it is often a little while before they are confident that you are coming back, and even a dog that has previously had no issues can express separation anxiety if left totally alone when they are not used to it.
I like to leave Perry's roller ball and Kong in his crate with the door shut for awhile before we go out. Although we haven't crated him in years, seeing the treats builds his anticipation so that he is very happy when we give the treats just before we go out the door. This technique will also work well if you are planning to crate the dog. 
He had free run of his foster mom's house while she was at work and was very good about it. He is not house destructive at all so that helps a lot! Because of that, I will let him run the house while I'm gone.
Oh and progress!! Pepper (my black cat) and Congo ate breakfast together today! Pepper even spilled some of his on the ground and Congo patiently waited for me to get his breakfast and didn't make a move on Pepper. I was so proud of Congo!! He even sat when I told him to right next to Pepper and of course I gave him a treat!
Pepper has lots of places to climb up on and escape from Congo so leaving them together shouldn't be too bad. I haven't taught Congo how to use the balcony dog door yet because Pepper uses it as a time out and potty area (his litter box is out there). Once they get more comfortable with each other, Congo will have access to the screened in balcony.
