I doubt #1 will help very much in your case; if the rubber is being punctured or worn through at the edges, a coating of paint--even thick elastomeric paint--isn't going to prevent that very well or for very long.
#2 or some variant of it is the correct answer.
#3 may work, but is clearly a stop-gap measure and may be wasted effort if you later decide to replace the front portion of the roof. Adding an unnecessary seam doesn't strike me as a particularly wise idea.
In your shoes, I would investigate the possibility of using something like
RV Flex-Armor or
RV Armor. I have no personal experience with either of these (nor any other similar products or processes), nor know anyone who does, but they do sound promising to me.