From Prophecies to Factions - The Transition

So, I recently got into Guild Wars and I'm making my way through the original storyline. I picked up factions because I love the extra content. (more area to explore, more options) but I'm coming up with a lot of questions as to how these 2 games have been merged together. I understand that my prophecies character can visit the land of Cantha by way of a ship from Lion's Arch but does a Prophecies character start the story missions same a Factions character? If I grab a boat to Cantha, at what point in the story do I start out?

Basically I'm just looking for what to expect on the move from the Prochecies campaign to Factions areas. And how do I on the boat over there? And how do I get Kurzick Armor? lol that armor rocks.

Thanks for the help.

Ch1 to Ch2 - you start on the "mainland" content - you miss 2 missions.

ch2 to ch1 - you start in lion's arch - you miss ~5-6 missions.

As the Canthan characters start in Lion's Arch when they come to Tyria, they will miss all the missions up until Lion's Arch, all 7 of them.