What I mean - is once the marbles are set up, before the user starts getting rid of them, work out the maximum possible score that he/she could achieve if they clicked all of teh right marbles in the right order.
i.e. For some sets it may only be possible for a user to get 400 points, whilst for other sets 500 may be possible.
This way, at the end of the game, you could calculate the users score on how many points they've got AND the percentage this is to the maximum.
If the maximum possible score for a full set of marbles is 400, and a user gets 390 - this is obviously better than a user getting 410 on a set with 800 possible. (But the current point system says otherwise).
This way users can aim to get 100% each time.
Make more sense?