Get the professional sander guys in to repair the living areas and kitchen but don't go too dark with the stain as it will kill the lovely grain in the matai. I'm thinking a couple of tones richer than the timber knots showing in your photo, definitely no yellow tone at all. In NZ stepping on to carpet especially in a kiwi winter is so much nicer than a cold floor board shock!!! A nice area rug for the lounge and you're done.

after watching my daughter and her husband agonize over the way their expensive timber floor has not held up well after 3 years, I would recommend tiles/wood look tiles with under heating. Their beautiful warm expensive floor looks like it always needs a clean and polish, not from neglect, they have cared for it well. One of the boards now has a slight and painful moan when it's stepped on :-( I grew up in a completely wood floor home and although it looked wonderful, my Mother hated it. ....and the mats ! Wood is a lot harder to maintain than tiles ,(no matter what the die hards say) the modern wood finishes are much better than they used to be.... But a piece of wood is rather arty no matter what it's used for and it does demand to be loved and cared for.....and if something goes wrong it's a lot more expensive to fix than sand and cement. Ultimately you have to be happy. BTW underheating tiles is warmer than timber :-)

We currently have a deck on the first floor over the garage. It construction is wood with a water proof membrane over, that is now leaking, with carpet that is used on boats over the top. What would be the lightest and best floor covering to use when we re do the deck?

my suggestions has the central entry and a small study off the living room...(twin desks provides more counter and wall storage and avoids sitting face to the wall) there's a generous laundry mudroom with direct external access, a bathroom with separate powder room, more space in the master suite with the window offsett for furniture and more privacy from views across the courtyard and reversing the wiw and ens allows for morning sun in the shower and the wiw creates a sound barrier against the guest room.. adding furniture helps suggest room sizes and there's various setdown spaces and extra storage throughout the house ...luckily there's plenty of room for more than minimum offsets to create a garden, alfresco, courtyard, screened spa room, entry, kitchen and laundry porches, garden sheds and drying areas and careful choice of building sizes allows for a neat gable roof with the extended eaves and a hip roof over bed 3 keeps the whole roof simple and economical to build