missing dog found and housebroken no longer

Question
Our 9 month old puppy went missing two and a half weeks ago.  We was picked up by animal control after being gone for two weeks and we found him at the shelter three days later- we had been out of town for a week of his absence.  He had been housebroken unless he got water or food during the night.  Since returning yesterday he has made my bedroom his toilet.  I have used OUT! Pet stain and odor remover, but he has pooped twice and peed twice in the area in front of my closet door.  His previous accidents (before being lost)had been downstairs near the back door, usually just pee, and only when he got water after 8pm. We aren't letting him spend mega amounts of time outside since we still haven't figured out how he got out of the back yard before-escaped or somebody took him.  Is he mad at me?  The stools have been loose, should I take him to our vet even though he is current on everything?  Or are the accidents and loose stools simply the stress of possibly being on own for last two weeks, then the shelter and then our home?  I would greatly appreciate your advice on how to quit the messes.
Thanks,
Jennifer

Answer
If he doesn't settle down, I would get him to the vet before the weekend. You are quite right about the stress.  He could have picked up something or even be from strange food.  Otherwise, you mayhave to retrain him.  

When you are around you need to keep a close eye on the dog. Use closed doors or gates to keep it in the same room as you are, and perhaps as I do, a short chain fastened to the computer desk. If you catch it in the act, give it a sharp ''Ah, ah, ah!'' and take it out. When you can't watch it, crate it.

It is only natural that a puppy resists its crate at first. What the puppy wants more than anything else is to be others, you, anyone else in the household, and any other pets. In our modern society, even if we are home, other things distract us from the attention an uncrated puppy must have. The only real solution is to crate the dog when you aren't around. The dog may be happier in its den than loose in the house. It relaxes, it feels safe in its den. It rests, the body slows down reducing the need for water and relieving its self. Dogs that have been crated all along do very well. Many of them will rest in their crates even when the door is open. I think the plastic ones give the dog more of a safe, enclosed den feeling. Metal ones can be put in a corner or covered with something the dog can't pull in and chew. Select a crate just big enough for the full grown dog to stretch out in.

Leave it some toys. Perhaps a Kong filled with peanut butter. Don't leave anything in the crate the dog might chew up. It will do fine without even any bedding. You will come home to a safe dog and a house you can enjoy.

A dog that has not been crated since it was little, may take some work. Start out just putting its toys and treats in the crate. Praise it for going in. Feed it in the crate. This is also an easy way to maintain order at feeding time for more than one dog.

The "shut the puppy in a safe room" is a fallacy. Very few houses even have a safe room. How many of us have a room with a hard surfaced floor and nothing else? Most rooms have electrical cords to chew if nothing else. In addition to destroying anything a bored puppy finds to chew, it may choke or have intestinal blockage from the pieces. I had a friend that left her dog in a "safe" room. It ate a hole in the floor covering. The safe rooms fail to give the dog the comfort of the enclosed space their instinct requires. Nor do they restrict activity extending the time the dog can go without relieving itself.