Jdog619;
Each fortress has various anti-dragon shields that need to be taken down, and a commander in a headquarters. There is an equipment set in each of the fortresses for Stone, Raze and Kali. If you get all that, then you know you've pretty much cleared the fortress.
There is an achievement when you complete all of the fortresses, but nothing for each individual one. I usually fly away from the fortress to get a general overview when I am done, and fly by each of the platforms in a methodical way (depending on how the fortress is constructed it may be easier to check out all the highest level platforms, then the next level down, etc). In dragon form you can see if chests are open or closed, and if you make a practice of breaking all crates and barrels, any you spot from the air mean that you missed something.
In the action RPG I of the Dragon, there was a spell that would reveal the direction of all opponents. Once activated, for a limited time you would see a glowing red/orange aura in whatever direction there were opponents. You didn't get a distance (unless they were visible onscreen anyway), but that made it much easier to track down the last remaining creatures in an area.
For the leader of the Red Hammer tribe, did you try going back to that cave? Maybe there are some goblins there, or huts outside, or something you can take out. Did you fight him again outside? If not, maybe that doesn't get trigered unless you have the quest.
I killed lots of quest NPCs before getting the actual quest (though not in this case) and didn't have any problems.
TheKingsWill;
A pale imitation deserves to die for the insolence of presuming to use my name.
