Very comprehensive post Oamanes, I just wanted to add some things that I thought you missed.
If I may. ;)

Quote Originally Posted by Omanes Alexandrapolites View Post
Unrest is caused by recent conquest of a settlement, governor's traits and enemy spies stirring up trouble!

Sadly, resolving unrest caused by the settlement changing hands in unresolvable and cannot really be changed without the help on a unrest reducing governor - sorry.
Of course the level of unrest changes over time, more specific is reduced by 5% every turn.

Quote Originally Posted by Omanes Alexandrapolites View Post
However, checking out your characters can solve unrest. Does the governor have unrest causing traits in his selection? If he does then get your calculator out and add things up! For every happiness influencing point which is positive, such as influence/subtraction from squalor, add 5% onto your totals unless a percentage is given and then instead add that on. Then subtract everything negative, taking away 5% per point of anything unless a percentage is given. If the governor's rating on your calculator turns out to be below 0 (causing more problems than he is resolving) then take him out and find somebody with a better rating.
Then again if one just wants to know the effect a governor has on a city, one just has to move him out of the city and then check the changes this causes in the city details scroll.
This is especially usefull if your governor seems like he is going to take the ship to the afterlife soon since you don't want to suddenly be confronted with a city with e.g. a runaway population or on the brink of revolt because the influence bonus is gone.

Quote Originally Posted by Omanes Alexandrapolites View Post
Cultural penalty is caused by buildings of a different culture being in your settlement. For example, if the Romans were to capture a Greek settlement with many Greek buildings then this factor would run rampant. It causes a -5% penalty per building that is not your culture with a 20% penalty for the governor's building. It does, however, reach it's maximum capacity at 50%.
I beg to differ on this point, if I remember correctly it is not that much a matter of number of buildings of a different culture but of the ratio between those and the ones of your own culture. Though I have to agree that the governor building has a greater effect than other bulidings.
Or am I mistaken? I think I read this somewhere in a guide, even being a quote of a developer.