When you recruit a new advisor, do you also earn the fortune and reputation tokens respective to that character? If not, how do you earn fortune and reputation tokens once you've spent your initial allotment?
Each adviser has a gold cost. Above that is a reputation cost that can be paid as an alternative. I don't know of any advisers that have fortune costs on them.
There are appellations that leaders can have that give a reputation or fortune every winter. At the end of each game, the winner can add a starting reputation or fortune to their leader (see page 20 of the rule book). Other than that there are not many ways to gain them.
If you want some small spoilers:
Spoiler (click to reveal)
Some Captain's Booke entries will give reputation or fortune tokens. Rarely they will give you the opportunity to add a starting reputation or fortune sticker to your leader.
They are a very limited resource.