It's cool I figured it out. It did work in getting the Jarls back to normal, unfortunately my game is filled with dragons now lol. I don't suppose there's a way to end the dragon attacks once they've started?
What? How dare you want your cake and eat it too!
Actually that's the whole point isn't, why else would you want a cake for? Anyway I digress.
The better way to do this is to reload to the point before you broke in, go get every single other gem, then:
set TGCrownGemsFound to 24
set TGCrownGemsTotal to 24
setstage TGCrown 30
Upon which the dialog for vex to proceed to the next stage of the quest appears. This is better than mucking with the main quest which you won't know if you screwed it up somehow until you attempt it 100 hours later.
Source: http://www.uesp.net/wiki/Skyrim:No_Stone_Unturned