For the Richard quest, it sounds like the one npc is stuck or bugged. Should have loaded from your previous saved game and tried to finish the quest again. Were you able to set the pig free?
I missed the quest form Jonah, but it sounds like you won't be able to finish it. I stole his gem but never used it, Vacca was not that hard to kill. You still got the salve to get the wyvern egg.
