If you do decide to go to Milford Sound you could always consider staying the night there. That way you could take your time driving in and out and you could go on a cruise first thing in the morning or one of the last ones of the day. Also
Real Journeys do overnight cruises which are magical. It is fantastic to be out on the Fiord as the sun goes down and hearing all the night noises and seeing so many stars. There is only one place to stay on land and thats at the
Milford Lodge.
I worked and lived in Milford Sound for a year and saw it in all it's glory and would agree that a rainy is great for seeing the waterfalls but if you want to be able to see the tops of the mountains then a fine day is the best time to go.
Ok I could go on about MIlford all night

, so will stop now. Oh Doubtful is also brillant. And it is possible to do the whole of the South Island in two weeks. I did it with my parents years ago and we left from Auckland and went down the West Coast and up the East.