I would enroll him into an obedience class and also get him neutered if not done so already. I would make him work for everything (not just treats) when he has to go out to potty make him down, he wants dinner make him sit, if he wants to be petted make him do a stay etc... Also teach him a drop it command this way you can get his toys away from him without a problem. At first when teachin the drop it I wouold always offer something in place of what he has (another toy or treat) so this way he does not get even more protective as he will know he is not "loosing" what he has he is just exchanging it. As he learns that command start slowly by lessening the treat or toy. Also EVERYTIME he growls you need to firmly scold him tell him NO VERY FIRMLY (or however else you scold) and totally ignore him for about 5-15 minutes. Being part pit bull (if so) they can be challenging so you need to establish that you are the leader. Border collies can also be chalenging and stubborn. As far as him waking up he might of been just challenging you but to be on the safe side I always check out the surroundings and let my dogs out to potty (as they too are like clockwork) so if their time clock changes I like to make sure nothing is wrong. At first I ignore them for a minute if they continue to wake me up I ignore them but get up and look around and then let them out. Sometimes their tummy might bother them or they have to potty and to be on the safe side I want to make sure there is no danger. And borders are very active he may be showing these signs out of boredom so an extra walk or vigourus game of fetch everday may help or agility or flyball!