Since I was confused on the mileage question I did something novel and picked up the phone and called SMS. Based on what I was told, by the rep pulling up the flights, was that I would get all my MQMs and GM Bonus miles, but I would not get the upgrade. I could live with that, since I know I wouldn't get a companion upgrade anyway and even if I got the upgrade and gave it to my wife for some brownie points, she would rather sit near me, go figure !
So after all of that, I went looking for 5 tickets instead of 2, since my wife's brother and sisters have now decided to go as well (family wedding). So I go onto CO's website, bring up 5 seats for the $260 per, but no matter what I tried, I couldn't purchase the seats. After calls to CO web support and their res line, I think we finally figured out why I couldn't get the seats. It seems DL changed the flight time of the first leg, and the CO web site still had not been updated. So after all of this, it's a moot point, since I can't get CO, either on phone or web, to be able to book those flights. So I guess I need to wait until CO is updated to see what the new price will be. My other option to keep life somewhat simpler is to book the nonstop JFK-SAN and be done with it. Thanks for the replies.