Oh I do know what you are going through. I had a tough time with Bentley, and I must admit, even tho Bentley is a year and a half now, we still having peeing in the house issues (and I rent an apartment too, so I worry about any carpet damage). But, in my case I do realize it is my fault, I live alone and had to work 40 hours a week, so he had to be alone all day (well, he has Bailey, my toy Poodle, for a buddy), at first I kept Bentley in the kitchen, as crate training just did not work out at all for us. But, I put puppy pads down and paper-trained him, and that worked for us. Good luck, hang in there, it will get better! It sounds as if you are really doing all you can. About the crying, maybe he is crying because he wants to be with Indy if the two of them are separated when you are gone? I know I could never keep my two apart, they have a bit too much separation anxiety for me to do that, so I keep them together always.
:flwr: