I've been thinking of a way to implement it. You may have to design them as a seperate quest entirely. I was thinking that despite the war going on, I could not imagine the overly competitive Clans from not trying to "one up" each other during the conflict.

Basically the clans offer up a mercenary contracts to help them finish off fairly dangerous or impossible missions. These missions could have very difficult requirements (No K.O.'s in your party, finish enemy with a specific type of attack, only use moogles, only use Dragoon classes, solo Marche missions ect...ect...) The missions are presented by a "contact" who only randomly appears cause the Clans don't wish for the others to know they need help. Missions could be about recapturing escaped prisoners, taking out powerful monsters used by enemy forces, or even secret rescue missions. You get very little for completing these missions until a certain point in the game when the Clan you've helped the most "rewards" you under the table with a special item (Spear of Cyril and whatnot...)

It could be used as a means for more hardcore players to get into and I feel it should be limited so it doesn't distract from the main game. Say you write out 3 scenarios for each clan, they are all avalible from the first time you meet the contact but the game should be programmed to have the contact only appear within the normal storyline about 4 or 5 times. So only if you stay consistent would you qualify for the right item. You could also make it a little more lenient if you wish.

I also had another idea for a side quest in the game but I'll probably PM it to you instead as I wish to keep it a surprise. But I want to hear your thoughts on this first.