Download and apply patch 1.4. Remove any Mods you are running before applying it
http://www.ubi.com/US/Downloads/Info.aspx?dlId=2172
You don't need any of the other patches listed.
Unfortunately you will lose any current mission you are in in career mode. Once you apply the patch in port you should be OK.
Several of the larger Mods improve the mission structures even more, but make the game a little more challenging. I use Trigger Maru Overhauled (TMO) and it really adds to the experience.
JCC