1) How does the command 'randomly discard/choose a card from the opponents'/your hand' (from people like agent, or the thief) effect organizations, factions, and long term advantage cards (like seals of the dragon, magical object) as they are shown face up (i think) and thus can't be randomly chosen?

2) Also, if you have such cards in play, do they count towards your 5 card hand limit?

ie, I have 3 combat adv cards, one organization, and one faction in play and I complete my exploration phase. I choose Advantage reward on a level 3 area. How many cards do I take?

3) if i draw the avatar of death (discard all cards from your hand)
does that mean i discard all characters and their enhancements (plot cards like romance, etc), organizations, and other advantage cards?

Or do i just discard all advantage cards that aren't organizations, enhancement type cards?

4... not really a hand question...) can I play divine intervention (or other such avoid encounter abilities/cards) on that encounter to avoid Avatar of Death?

Well let me see if I can answer some of those questions. I do not believe that anything that you have played on the table counts as being in your hand, therefor you can not be made to discard them or have them stolen when the card states from your hand. They do not count toward the handsize. And if you have a card that allows you to escape an encounter that would make you discard your hand, then you would just play that to keep the rest of your hand. Hope that has helped some.