I like the decision to turn the wandering monster into the masked figures. To some degree it could be seen as going easy on the PC--a combat encounter probably would have finished him, but it also coloured the campaign world in a nice way and raises questions (why did they follow him? just who are they? what do they really want?)
I'm really interested in seeing how these rules play out in the long term--ie what happens in the world, and what the rules imply about what is going on in the world. Question: in your mind, is the world recovering or is it dying?
What happens to a hex if Trouble is left unchecked? Does it fall under the influence of Torog?
Nitpick: Hey, why do roads matter to flying units?
The idea of PCs and their henchmen seems to be leaning toward a "troupe"-style play. Have you looked at the way ARS Magica handles that?
Skills - how many are PCs allowed to have?
I'm looking at the Hexcrawl generator. You used Nentir Vale from the DMG, obviously? How did you square the random generator with the features that are already there? Things like how the Random Generator can create settlements, but the map already has a few.
There are two tables for Content, the one containing "Terrain Feature, Resource/Settlement, Ruins, etc...", and the one containing, "Artefact, Gate, Map, etc..." When is the second chart rolled? I have been rolling for each of the listed features in the second chart each time I got a 75+ on the first chart.
Speaking of the second chart, what exactly do you mean by "Tricks"? How are tricks different from traps?