Eternal Boundary => Harbinger House crossover ideas.

I've just finished running my tabletop group trough the Eternal Boundary. Before the campaign is over, I'm planning to run Harbinger House and Faction War; the big three of published Sigil adventures. One issue that I imagine might be a problem is that both EB and HH begin with the PCs investigating a murder mystery. I don't want my players to feel that they're largely rehashing the same plot material over again. I was wondering how other DMs might have married these adventures together in their own campaigns. Please share the fruits of your wisdom with me.