Sorry for chiming in late, just saw the post.
Excellent decision to do the kayaking in Doubtful Sound - this is a truly magical place! Did the 3-day trip last year (Jan 2013) and greatly enjoyed it. Yes, there will be a lot of sandflies!
Don't know what your luxury level / price range of accommodation is, however, stayed at the "Lazy Dolphin" hostel in Curio Bay and can highly recommend that for your trip from Te Anau to Dunedin. Very friendly, comfortable and laid-back and you can swim with wild dolphins right there at the beach!
Enjoy your trip, it is a really beautiful country (will go there myself again in a couple of weeks).
Have safe travels
Primenumber