B1. The last time they saw each other was when the Iron Islands rebelled. Ned was always more of the quiet loner type and it took someone like Robert to drag him out of his shell. Beside that, he never much cared for the society of the south. After his brother joined the Nights Watch it made sense for him to stay in the north as his heir was still a child and there must always be a Stark in Winterfell.
B2. Probably not, She seemed to think comparatively little of him next to his fantasy of her.
B3. Aye, it is debatable that the family insanity did indeed pass her by.
S1. They filmed flashbacks (or possibly a prologue?) for the first season but cut them all and any other opportunities to show such things have also been left out. Clearly they would rather keep the focus on current events.
S3. Yeup. A 15 year old acting like Jon makes a lot more sense than an 18 year old.