It's not something I easily worry about, but I think you might have overpowered the natives.
Currently, Armed mounted braves have 4 strength and 3 speed, while cavalry has 3 strength and 2 speed. In addition to that, cavalry suffers all kinds of penalties on terrain, while AM Braves retain their attack bonuses.
I think Europeans are supposed to have stronger cavalry than natives.
I would suggest giving cavalry their power of 4 back, and reduce the strength of AM Braves to three. Their terrain bonuses, and the terrain penalties of European mounted units, more than balance that out, in my opinion.
Also, I'm not really a big fan of the changes to all the experts and masters. If you introduce all kinds of penalties for working either outside or inside a settlement, it will give the player the impression that all his colonists are servants and criminals. Also, expert classes are not strict upgrades over Free Colonists anymore, which can force the player to clear specialties all the time. Your worker units become really inflexible this way.
Edit:
I've also noticed that you gave native units a base strength of 1. This would give AM Braves a strength of 5, Mounted or Armed Braves a strength of 4, and regular braves 3 Strength. That would be
extremely strong.