During the second scenario of the second league, we obtained a rather large amount of clue tokens. We actually managed to grab all the clue tokens, but we ran out. My character got 4 clue tokens, but only two were left in the bank. Do I grab the 2 remaining and leave it at that, or do I keep track of spare tokens on a piece of paper?

(Tried to search for this, but I didn't level my searching skill at all.)

Keep track with something else... for example Eihort tokens work well.

or yellow signs

Ok, I was just making sure that I was able to aquire those tokens instead of being shorted... Thanks!

It might not be true for general games (though how you get that many clues normally without being in a position to have won ages ago...), but the league FAQ specifically states that the clue supply is finite for the scenarios (it's in a general bit above Scenario 1).

Ah! I knew I read that somewhere. Thanks! Oh well... what's a couple of clue tokens.

Yeah, once you've taken all of the clue tokens, that's it, according to the league FAQ, but again, by the time that you're doing that well, you could probably just win at your leisure.

It also says that clues used to note things (i.e., on some Rumor cards) don't count toward this, so, if you need a few, you're allowed to put generic markers there and put the clues back in the pool.

That being said, though, I think that it's a good idea to count up all of your clue tokens and check them against the component list in the AH rulebook. If you've lost a few and don't know it, then you're shorting yourself a bit if you don't know that when you run out of actual tokens.