Well, so far so good. If pup has not shown a great desire to chase and play with the adults, you are off to a good start. I'd just be sure you can supervise the first few births and keep an eye on jr. Sounds like he is the kind of dog that will respond real well to your admonisment if he was to get too close. But at the first sign of trouble, either too intense an interest in birthing ewes, or not enough respect, tie him up when you are absent (or move him to another place where he cannot access the birthing ewes). lambing is pretty exciting for a young dog and all you are trying to do is make sure the first lessons learned are the right ones.
You will quickly know if he is one of the rare few that can be trusted.
As to his barking at the ewe...that made me grin, as I have his grand sire, and that is exactly what grandpa will do if he thinks the sheep are in the wrong place, he barks at them. It is pretty handy because it will serve to alert you when they get out, other times it will annoy you when pup decides the sheep should not go through a certain gate. In the bigger scheme this behavior will be very important when a predator arrives and the dog attempts to round up the flock and take them to safety.
You may never know exactly what it is that triggers the barking, but as long as the sheep and the dog resolve the issue peacefully is all that matters.
Tamarack Prolific and Ile de France crosses