So... I just got out of privateer's hold, met the the blades girl, and joined the knights of the dragon. They gave me a quest to go kill a nightblade in a dungeon. Not very far into it, I fought a werewolf, and when I rested, I got a dream involving some naked guy and some words I didn't hear very clearly. Did I catch lycanthropy, and If so, should I reload a save of before I went to the dungeon? As a rather new player, I don't want to be severely limited in what I do just because of some side-quest that might be better off being ignored.

"You dream of the moon, and of a man who is less than a man."

Am I right? Yes, you contracted Lycanthropy. If you don't want the awesome gift of Lycanthropy and remain a boring person, then reload and replay.

However, you do have 3 days before the change becomes permanent. (Cure disease) cures are available at any temple or by using a potion or spell.

I didn't hear the words clearly enough to understand them, but from looking at the wiki, I did catch it. Also from looking at the wiki, it doesn't look too bad, I think I will keep it, but will it break the MQ in any way?

While we're at it, I fought LOTS of vampires and ancients.... some of them hit me. How do I know I got vampired *before* turning into one? Is there a dream too?

Yes. You'll see

Slightly off-topic question, When I kill a werewolf for a quest, will it tell me when I've killed the right one? I've killed a few in this other dungeon and I don't know if they are the right one or not.

Yes, you will get a message when you find the right one.