I've been traveling quite a bit through the game, kind of aimlessly. I've come upon quite a few forts that I've cleared, and haven't really found any quests with instruction to clear any forts. Am I going to mess up the story line or my gameplay this way? Figure I'll stop doing so now, just in case.

Thanks!

This will not effect misc quests, as they find random places for you to go and complete the objective. However, this can effect set quests that require those dungeons. The only problem you will face is that you can re-learn any words on the word wall that you had already found, getting the second or third word in the shout, and that the enemies will respawn. There are no major repercussions from clearing out the dungeon early - you will still face enemies.

Actually you don't have to worry about it. If you are sent somewhere to do something after you had already cleared it after the quest is assigned you can complete it if you meet the conditions. Generally quest items can't be sold, so the only thing you have to worry about is if you find a unique item and you drop it some place and forget about it. So if you find something unusual be sure to keep it in case its a quest item for later, or better yet just leave it. Quest items don't have any value and no one will buy them, a clear sign you probobly need it for something.

This is why having a house is so useful, you can store all the unusual stuff you find in the world there.

All, or at least the vast majority, of dungeons respawn.

Most misc. quests are just there to give you an excuse to visit random dungeons as it is. Any major story related dungeon will be locked until you get the relevant quest.

Thanks!