I wanted to post a follow up on this. I met with the owner of the roofing company this morning. He was very understanding and apologetic, and is going to redo all the work. He is going to have his crew come back, pull the shingles and nails from over the eaves and redo it all with shorter nails, fix a rotten spot in a roof board they overlooked, and redo the flashing. I found out that the barge rafter was never formally put into the work agreement and he was pretty ticked with his people for not only doing the work without proper documentation but also having someone do such a crappy job. He asked if I knew any contractors who could do it and I told him that I've been doing my own carpentry work for 40 years now---I only allowed this to be built because I was out of town. So he is going to sub it out to me to redo the rafter, which I will and do it correctly. As for the OSB, he assured me it was rated for exterior use so I am going to let it ride and paint with a good thick coat of paint. We all parted ways with a handshake and an agreement. I am glad I'm not in his shoes though... that's going to be a lot of work on their part to correct all of it.
Thank you everyone for your help. It's been a long time since I've been able to come to a forum, post a question, and actually get usable information.