I find the idea of a gate clue chart intreguing and it would be easy(ish) to impliment
The way I envision it working would be the clue deck is divided into 3 roughly equal parts (approx 25 cards per type? see discussion below). When a clue is discovered a token (glass bead) can be placed on a chart (for the entire party or for the individual, I suspect the party is better) of all possible clues. When the investigators had gather all three clues relating to a given gate it can be sealed. The clue cards can also be discarded to gain a bonus depending on the type of card. This means that early on the investigators probably won't be able to seal any gates but later they can close lots of gates. (If this rule set proves to be too easy the investigators could be required to spend a clue to add a token to the chark Otherwise, a "key clue" system could be added whereby the investagators must spend a relevant clue card to seal again in addition to the rules above. In fact, this rule may be necessary for larger groups as there is not other way to scale the difficulty of sealing gates).
Looking over the board and card decks to develop the clue deck I learned that there are 26 locations (divided into 9 neighborhoods) on the board, 8 dimensions used on gates (and 1 only on monsters), and 4 colours used 5 times. with 1 card per location (26), 3 per symbol relating to gates (24) and 6 per colour (24) a roughly equal deck of 74 cards can be produced. But such a deck would ignore the moon sybol (only has monsters) and has a disporportionate number or colours. (while the colours would have been necessary for my former system I think their numbers can be scaled back.(possibly to 3 per colour). I also think that it would be good to have clues relating to the moon symbol. I noticed the number of monsters with a particular symbol are not proportional (although their appears to be a relationship based off of their dificulty). Previously I needed to balance the number of symbol cards to facilitate gate sealiing, but with the chart system balance becomes slightly less important. Therefore I think a few symbol cards can be added to the deck. I'd also like to add some miscilancious clues.
so here is the deck as I envision it at this point
-26 nighborhood cards (3 per neighbor hood, except French Hill), grant an +3 bonus on checks in the given neighborhood when discarded
-12 colour cards (3 per colour), grants a +3 bonus on check in corresponding dimension when discarded
-30 symbol cards (3 per symbol, including moon = 27, +1 moon, circle, and hex) +3 bonus on checks against corresponing monsters.
-7 misc cards (help find particular clues and unique items?)
for a total of 75 clue cards
A total of 21 cards must be found in order to close all the gates with this rule system, but redundency of cards means that a larger number will be needed gain a victory (if anyone is good at finite/probability theory I'd like to know how many cards are needed to sucure a likely victory). ( 30 are required for a seal victory in the regular game).
I'm still not sure what a fair bonus on discarded clues is given the increased difficulty of matching a clue to a situation.
A far as producing a story is concerned, I think that by using the fact that all monsters of the same type have the same symbol and all gates of the same type have the same symbol a "story" can be peiced together for each symbol in the flavour text.