So, I've been lazily been completing steps of the main quest every few levels. A few days ago, when infiltrating the Thalmor embassy, I ran into some issues. After recovering the two bits of evidence, I freed the prisoner from the cell in the dungeon. But he just stood by the trap door and wouldn't open it. All of the quest objectives were complete, but the quest itself wasn't completing.

Using the console I was able to unlock the trapdoor and escape, as well as complete the quest using the "setstage" command. But there has been a snag, that I found out several levels later, when trying to talk to Jarl Balgruff about using Dragon's Reach to catch a dragon...all the NPCs that were in attendance at the party with the Thalmor are still stuck in their "party" dialog. For example, when I talk to the Jarl, all I can ask him to do is cause a scene.

Anyone have any ideas on how to get around this?

since it's probably too late to re-load a save you might have to use setstage again to trigger/advance some of the quests during the main quest (any where npc's involved in prior quests were 'skipped').