1) In addition to what Dutchman said, you also need to explore the ruined homestead thoroughly--make sure you read the graves in addition to getting the diary and reading the books in the library (talk to Garyeth.)
2) You won't get the note about Kayanna until the day AFTER you were supposed to meet her and she didn't show up. You have met Japsworth at the bar, first, haven't you?
3) I think you misunderstood Prospero's dialog--the person you're after isn't at the beach, she's in the old dwarven mines--located in the south-eastern-most corner of the South Woods.
4) I actually don't know if you can give anything to Kit or Ina...I've never tried it!
Blackthorne might know though.
5) No, the broken stairs are just decoration.
There's nothing upstairs in the graveyard house. Try searching the hole in the stairs though for a little secret plot element.
6) The beehive in the Volksville woulds doesn't need to be smoked out, just agitated somehow. Try hitting it with a stick.