I was struggling with my large cities late in my last campaign, a big help to the unrest problem turned out to be enemy spies. Finding enemy spies in my cities and killing them or at least kicking them out would drop my unrest from 30-40% to 5% or none. Oftentimes where there is one enemy spy there are 2 or 3 more as well. Try some counterspying, not only will it help drop your unrest, it will also give some nice traits to your governor to help keep the spies out. Just a thought if you haven't tried it.
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