After a week worth of worrying and patrolling my city's I have completed both sides of the story and as far as I can tell both saved games have been without inccedent for 3 real life days. I have done everything from fast travel between towns during the day and night,waited in every town till dark,went in and out of shops.its safe to say that the main story completion seems to be the final nail in the coffin of random attacks.as time goes on there are starting to be posts on diffrent forums that are also experiencing this.so I urge you to try it out,and avoid the main city's until you do(it's possible on both sides of the story to never step foot in towns during the main quest).come back here and report your fidnings when you finish so we can maybe get a full account on other peoples saves and not just mine..there is light at the end of this genocidal tunnel!
On a side note,on the dawngaurd side save, I completed the companions quest and also never once had an attack occur while going in and out of whiterun doing and turning in quests.(about a month or so of ingame time