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.

I'm guessing you are from NZ (kiwi) :) The handy sanders did our floors - http://www.handysanders.co.nz/. They did an AWESOME job and are reasonable priced. I would definitely recommend.

Is your stone veneer to be laid on a slope? I would want to see an example of that beforehand. The stones in a sloped wall are still set horizontally, but the veneer will have joints that look skewed if laid sloped so it could look quite odd.

Which would look better tiles or glass and what colour? Would it be best to cover the whole wall, half wall under the range hood or just between the range hood and cooker?