If I use the DarNified UI quest pop-up remover am I missing any information? Is everything I would have read there in the quest log? And does it remove all pop-up messages, or just the quest updates? What about messages that user-made quests add? I just don't want to unknowingly miss something.

Nope, it just suppresses the quest pop-ups (you'll still get the little sound when a quest updates), but all information in those dialog-boxes is readable in your quest-log.

Okay, thanks.