As I posted in the cheesy lyrics thread, this song has a lot in it about Bono and Ali's personal relationship. I'd say this song is more openly about Ali than any song since Spanish Eyes.
The sleeping in the street comment is one I've seen him refer to on other occasions. He said as a teenager, after his mum died and he and his dad weren't close, he spent a lot of time at other people's houses, whenever they'd have him, and that he slept on floors and sofas everywhere, "like a stray dog." He has also said that Ali's family was very good to him, taking him in like a stray, feeding him, driving him home at night. He still says that Alil's family are like his family, and her parents are like parents to him. So there's no question to me that's where that came from.
Also the "I don't want to take a chance, on losing love to find romance" part. That tells of their longterm marriage too, and how while other stars throw away the true love of their wives for a quick fling for excitement and romance, Bono doesn't want to lose real love for that.
Then there's 'brown eyed girl across the street... I thought this was the one for me, but she was already mine"
So this is one of the easiest U2 songs to 'get' if you know the background. This one is about the love and devotion of Bono and Ali.
Why the 'little sister?' well, maybe it's just a pet name or something.