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Welcome! It's very admirable that you want to improve this dog's life.
Can this dog walk on a leash? Exercise is one thing that will help make this dog more manageable and more trainable. Running in a pen isn't near enough exercise for a border collie. A border collie is a working dog, they were bred to work. Nowadays, many people that have border collies don't work them, so they have to replace the work with exercise.

The problem is, if he hasn't been trained to walk on a leash, he may end up pulling. Pulling on the leash isn't good. So, any time he pulls, you should really stop and "be a tree" to teach him that pulling isn't going to get him anywhere. BUT, if you have to keep stopping every time he pulls he's not really getting any exercise, right? So, start with several SHORT walks a day(if he is having a pulling problem) so that he (and you) don't get too frustrated.

Even as you are training him to walk on a leash correctly, you will still need to increase the amount of structured play and exercise that you give him, as the walks won't be giving him much exercise when you're in training mode. Many dogs won't run and play in the yard unless someone is out playing with them.

In addition to exercise and walking, you can start doing some short training sessions. Training is like exercise for his mind, and that can use up his extra energy, too. But, the same with walking, if you start with lots of short sessions a day then you (and he) won't get frustrated or bored. And, training can help create a bond between you and the dog.

Start with sit, and maybe down. We taught sit by holding a treat in front of their nose and moving it up/back over their head. That way, to keep their eyes on the treat, they kind of naturally lower their butt, so they can look up at the treat.
It's really good to lure them to do what you want several times first, before giving it a name. So, try getting him to sit like this before saying sit. After you are pretty successful at getting him to do the behavior, you can start adding the name. So, he sits, and you say "sit". He still gets a treat every time he does it, but you are just giving the behavior a name.
For down, get him to sit first, and then hold a treat in front of his nose, and gradually lower it to the ground.

As for housetraining, the best way, in my opinion is to PREVENT accidents by watching him super closely. Don't give him any freedom in the house, have him in your sight at all times. That way, when he starts to sniff excessively or circle around you can take him out to pee/poop. The more often you can PREVENT accidents, the more likely he will see outside as the only option for peeing/pooping. Also, don't scold him for accidents inside. It's your job to teach him outside is the right place. Dogs generally will pee or poop wherever and whenever they are when they need to go. So, if you get him to the right place, when he needs to go, you'll be doing both of you a favor.

Other things that make dogs well mannered: teaching them not to jump at people (even in fun), greeting people politely, etc. All these things are discussed at the top of each forum pages in "stickies" which are permanent topics. Check some of them out.

Be patient and consistent, as this dog has had a long time to get set in his ways, and it will take time and hard work to help him.
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