Great Pyr "Accident" Issues

My girlfriend and I recently adopted a nearly 3 year old Great Pyrenees.  Since we are both at our respective homes for the summer (both still in college), he is living with me and my parents and sister for the time being.  Despite only being around me for a minimal time though (in the grand scheme of things) he seems to suffer from something similar to separation anxiety when I'm gone.  I'll try to fill in background information in the following paragraph.

I have had him since July 6th.  He was at that time staying at the previous owners' parents house where he had been for around 2 or 3 weeks.  He spent the first night with my girlfriend and I at her parent's house, and had no issues.  He then made the 5 hour car ride (with stops of course) to my house where he has been ever since.  From the moment we picked him up, he does not stop following me (not a bad thing...just filling in the back story).  If I go outside for whatever reason, he typically either waits at the door or watches me through a large window we have in one room of our house.  The problem arises when I am gone for any length of time.  Typically if I'm gone for anything more than 20 minutes, and he has free reign of the house, I come back to find a mess either upstairs or in our basement.

To my knowledge he has not had any issues when I am around, and only 1 (of several) has been on the main floor of our house.  All the rest are typically upstairs or in the basement as I said.  Another kicker is that if he is kept in my room while I am gone, he does not have issues...gener ally just lays/sleeps on my bed or at the foot of my bed.

Things that could cause it(?):
He was/is on a diet of Old Roy Lamb and Rice Meal.  My girlfriend and I tried to change it to Purina Lamb and Rice, but upon doing this, his stools became more runny and had a green tint.  When we were trying to swap him over, we spent about 10-12 days gradually adding more Purina and less Old Roy.  I didn't realize his stools were affected until day 7 or so, and didn't attribute it to the food until a few days after that.  He has since gone back to all Old Roy.  Side question...any thoughts on Old Roy?  I've heard arguments both for and against cheaper dog food.
Shots.  When we got him we thought he was up to date on all his shots.  I called the veterinarian to double check though, and they said that they had not seen him since his shots as a puppy (March of 2006 I believe).  This should all be resolved by the upcoming Wednesday.
Food again...My family has another dog, a 8 year old Golden Retriever who eats Purina of one kind or another (not sure which type).  While my Great Pyr does not normally go for my family's Golden's food, there are opportunities when he could get into it without anyone knowing.

Any [more] ideas on what could be causing the problem, or do you have anything to recommend to break him of this habit?  My girlfriend and I go back to school in a month, and I'm not looking forward to replacing all the carpet in my apartment when I move out next year.

Thanks

Hi & welcome.  I'm Marie, mom to a Golden mix and two Pyrs that you'll see listed below.  Both Cass & Sammy came to us as adults and they both are very, very attached to us also.  I think that seperation anxiety issues are common in re-homed pets.  I have to think that in their shoes (paws?) that I'd feel the same way.  For Sam & Cass we've just made a point to keep them as close to us as is possible anyway to allow them time to adjust & feel more secure.  Also, obedience work with lots of treats & positive reinforcement as well as trips out to socialize help, too.

Regarding the "accidents" in the house.  I would do a few things.  First, you may want to have a stool sample analysed by the vet for coccidia or other parasites that might be causing him trouble.  Then if all is clear, I'd slowly switch him over to a really good quality food like Innova or Wellness (you'll find more info here on the food forum).  They eat less of these foods so they poop a lot (seriously, a LOT!) less than they do on the foods that have so many fillers like wheat, corn, etc.  Then he won't have to go as often or as much and he'll have healthier stools, too.  The main thing though that I'd start soon is to crate him when you're going out for a little while.  Dogs don't like to "go" in their den, so that should help him learn or re-learn his housetraining quickly and hopefully avoid him getting entrenched in the habit of pooping in the house.  I'd start him in the crate though at first when you're home so that you can see how he handles it.  When we first adopted Cass & Sam we crated them at night (or tried to  ) until we could see if they were housetrained or not.  Cass was fine with it, loved her peanut butter stuffed Kong treat and went straight to sleep.  Sammy though became frantic and immediately started to pull the fur off of his leg with his teeth.  That was the end of crating for Sammy, but he's housetrained and fine at home alone so it worked out.  Anyway, that's why I'd suggest that you try the crate with your boy while you're around just in case he gets too anxious like Sam did. 

Congratulation s on your new addition and thank you for adopting him.  I'm sure that he'll be a wonderful buddy for you & your girlfriend for years to come.  Oh & I'm glad that you found BPO.   

I don't have a pyr but wanted to welcome you to the board and congrats on your new addition.  Is there anyway that you can go back to your apartment a week or so before school starts so that he could get adjusted to the apartment and the sounds of the complex?  That way you will be there to help with his adjustment before you have to go to class.  Can you use a child gate in your bedroom door to let him see the rest of the apartment but kind of keep him confined?  I will second Marie's suggestion on the Innova.  It's an awesome food and my two having been doing great since I put them on it.  That's all I can come up with right now.

How much food should I be feeding Harley?  I haven't had him to the vet yet so I'm not positive on size, but I believe it to be around 135-145 pounds, and he will be 3 at the beginning of November.  Also, how much food would I be feeding him if he was on something like the Innova dry dog food (is that what everyone is talking about or are you feeding your dogs the canned food?).

Just curious because I'm trying to see how much more expensive it actually is.

Currently he is getting approximately 3-4 cups of Old Roy a day, plus whatever Purina One he scrounges from Moses's (the golden retriever) bowl.