We are certainly not experts, but Patrick & I had that same problem with our little girl, Toto! We discovered that if we put our hand towards her chin/chest area rather than towards the top of her head/neck that she was OK with that and gradually she allowed us to put our hand over her head. She still won't "come"! She is very stubborn ... but the running problem was much harder. We even had a trainer come to our home to work with her. The only way we can get her to stop is a very, very stern "Stay!!" At that she will drop in her tracks! We hate using that tone of voice with her but it's the only thing that works for us. It's very frustrating when they run like that and sometimes for their own safety we have to use methods we don't like ... loud, angry voices are extremely upsetting for her because she doesn't hear it in our home. As for the "delicate" problem you have with your little Jack ... thank God we haven't encountered this with Toto [she is 21 months]!!
There are many experienced people on this forum who can probably give you some very good advice. Welcome, and looking forward to seeing pictures and hearing all about your baby!!