How can I stop my dog whining when I leave?

A little background - my dog is a long wire haired Jack Russell, aged 12 and I have owned him a little over a year. I acquired him as I used to work for his previous owner of 10 years and part of my duties was taking care of her dogs. A few months before my employment ceased with Sams previous owner she offered him to me as her only other option was to have him put to sleep. Her only reason for this was that he was often wandering off on his own and getting himself and the other animals injured. (Basically, he lacked attention from his owner). He lived in an outdoor kennel his whole life with 3 other german shepherds and was obviously missing human interaction. (Due to him living outdoors he has remained very fit and healthy and is very simillar in fitness to a 7-8year old at least). Whilst he was with this previous owner, if ever the dogs were let out of the kennel, Sam was usually locked in a stable on his own to prevent him from wandering off the farm. He would whine and yelp continuously. Anyway, I took him as I'd grown close to him and couldn't bare the thought that he'd be put down simply because she didn't have time for him. He's taken to me incredibly, has totally disregarded his previous owner and can't seem to bare being apart from me. My boyfriend also worked here and has known Sam longer than me but Sam still prefers to be with me. I can't leave our house for 5minutes without him whining and tearing at the door, jumping at the doorhandle and windows. I've tried leaving him with his toys (he LOVES ), I've left him with plenty of food, water, bones, chew toys that he loves, dog chocolate drops and he is totally uninterested in any of them until I return. I've even tried not feeding him in the morning until I go out to see if this will coax him to eat whilst I'm out but again he just whines and waits for me to return. It's not even as simple as him not wanting to be alone, as I said previously he's known my boyfriend longer and gets on very well with him but even if I leave the house by myself, leaving Sam with my boyfriend, he wanders around aimlessly whining and crying, on two occasions he has peed on my partners leg (uming he's telling him he's angry that my boyfriend has sent me away?) Before we or I leave Sam in the house by himself we always take him out for a proper walk, making sure he does not need to use the bathroom, has worn himself out, etc. I don't leave him for long, 3hours is the most I have ever left him. I just don't know what else could be wrong and how to fix this, it's not necessarily so much that it annoys me (I'm not around to hear the whining) but it distresses me that he gets in such a state and I avoid leaving the house for simple things such as grocery shopping and send my boyfriend out instead. Help, is there anything I could do to help ease his stress other than medication?