The game's content is identical to the older freeware version. If you need a walkthrough you'll find one here:
http://gamesolutions.efzeven.nl/nelly-cootalot-spoonbeaks-ahoy-walkthrough-alasdair-beckett2006/

Use the book about birds on the coot in Bjorn and Olafssen's store

Arrange the alphabet (by clicking on the two letters you want to change places) in the graffiti puzzle that instead of "ABC..." and so on it says
QUIK
GOWD
SLVA
NCBT
HEPR
YZJM
FX
Then click the "read" button below

Give the pass to Blind Jimmy Thimble and go past the barrier

Let the ladies believe you are in the rocket that just flew away

Awarded when the cutscene with Nelly and the spoonbeaks on the beach plays

Pick the top right tattoo (skull with crossbones) and show it to Friday

Read the board on the right end of the market street until the text repeats

Win the main prize of hook-a-duck with eight caught ducks

When you get to pick a drink, start at the top of the list and exchange it for the one below it until you reach the cat guts

Trapped by the baron, pick the following replies:

• I can help you!
  
• I could give you information...
  
• I'll tell you about pirates.
  
• Pirates have a deep secrets... (yes, typo in the game, shocking)
  
• Secret Codes...

Use the shovel on Friday and Captain Rehab in the bar (the latter only counts when he accepts you as a pirate), Mme Leatherette (Store of Babylon), the bird at Bjorn and Olafssen's (after translating his speech with the book), Bjorn and Olafssen themselves, and Blind Jimmy Thimble (gatehouse to Saul Island)

This one is for getting all the others