I am a little confused over rule 9.3.3. When it says '...added to the Event Box...', does it mean the 'Event in play' box or the 'Available plot' box?
"Event Box" should be "Available Plot box" everywhere in Rule 9.3.3.
Does it mean each time WMD is added to the available plot box, an equal number of numbered plots must be removed and put back for each WMD plot used?
Yes, so that when playing against the bot there will always be exactly 6 Plot markers in play (either on the map or in the Available Plot box).