First of all, it's not clear what happens when Assassins inflict the last 2 wounds to other characters with their ability (taking the rank token and being captured).

Have the other character the chance to play their ability before resolving the capture? If so, it would be a very bad idea to use this ability against an Elder to capture him, but if they can't use their abilities, it's a perfect counter to that same Elder ability.

Also, I'm not sure whether I understood all the rules concerning tokens. The number of tokens of every allegiance seems wrong. 13 tokens with each clan icon? At most, there would be need of 10 (playing 11 people, 5 in each clan, 3 of them with 2 clan icons each, the other 2 with 1 clan icon each, plus the Inquisitor taking 2 icons of that same clan).

For undetermined allegiance tokens, the maximum would be 24 (playing 12 people with a Mage and an Alchemist in each clan, 3 characters from each clan with 2 undetermined icons, and other 3 characters from each clan drawing undetermined icons because of the staff), and there are only 20. If there are tokens in excess for clans, why not for undetermined? Am I missing any rule here?

First question involves the Assassin ability, and players can ony use their ability tokens when being attacked directly or intervening, not when dealt damage due to another player's ability. Therefore, the other player in your example cannot use their rank ability when forced to take their rank token, and they are captured.... and yes, it is a perfect counter to that Elder ability.

As far as the tokens go, there are extra in the box simply due to the possibilities involved with both the staff (as you mention) and the choices available to an Inquisitor player, who may pick any of the icons for their allegiance tokens. The sheer odds against actually needing all those tokes is rather high, but the printing space on the token sheets made this the best outcome, I would think.

Hope you're enjoying the game.... we certainly are!