Retraining a dog who is paper trained during the day

Hi, any advice would be appreciated. We adopted a dog from our area shelter. He is just under 2 years old and holds his 'business' during the night with no problem. He picked a spot just outside our bathroom for his 'business' while we are away at work. (not crate trained as our vet felt his separation anxiety made him a poor candidate for this)
We put puppy trainer pads and/or newspaper and he only goes there while we are at work. In his mind he is being good, and he is since he only goes there. The thing is we feel if he can hold it all night, maybe we could train him not to use the paper during the day and to wait until we come home to take him out.
So the problem is that he has picked this spot, and that we are not home during the day. He has his routine that has helped the separation anxiety (kong, no fuss when we leave etc) so now we are ready to tackle this issue.
Thanks

One of the reasons he can hold it all night is because he is sleeping. By paper training him, all you have taught him is that it is ok to go potty in the house. He doesn't know that he is supposed to have a pad under him and now he has picked a new spot to do his business in the house, only no pads, but he doesn't know the difference. How bad is his separation anxiety? Have you ever tried to crate him?

Although moving a dog from paper training to outside training is not easy, it can be done. What you are going to need to do is slowly (and I mean slowly) move the paper closer and closer to the door. While you are doing that, also make the paper section a little smaller each time you move it. Eventually, you are going to move the paper out the door and into the yard. Praise-praise-praise everytime your dog does the right thing. Great jackpot treats when he is going outside. Then slowly completely delete the paper.

A dog with real separation anxiety is not always a good candidate for crate training. It sounds like you have done a terrific job with his SA. Putting him in a crate at this point might reverse the progress you have made. That being said - I am a big believer in crate training, but to the SA dog - it is not always an option. If you have a crate, however, you can see how he does in the crate with the door open. Many SA dogs like a crate as long as they are able to get out at will, because it makes them feel safe.

If he is doing well in the house except for the paper training, I would try the above exercise and see if you can get him to the point where he will only go outside.

Good Luck!!

Wylie tried to bite the crate and jumped up and kept hitting his head on the top when we got him into the crate. this was with the door open. With it closed he tried to bite the crate so much that he actually got his jaw caught on the wires as he had bent them with his biting. I had to extract the wire very carefully. This was while we were still home and I spoke to our vet who said not to even try leaving him in a crate when not home.
We tried confining him to the kitchen but he jumped one baby gate and when we put one on top of the other he jumped until he toppled them and got out anyway.
He follows at home and the first month or so would urinate when we left, chew the sofa cushions, whine, chase his tail etc. We came home to a mess every night. We followed the advice of the vet with not making a fuss when leaving or coming home, leaving the kong and lots of chew toys, the radio on, a light on now that it is darker at dusk etc and slowly he is ok with us going to work.
He actually waits for his kong and no longer bolts to the window as soon as we leave. Only when the routine changes does he get panicky. Even if my dh works later than normal he will start to pace and whine. The vet also said since he is a shelter dog he was paper trained and it would be hard to break. He said we should work first on the SA.