You will absolutely love Chile. We did. So much so that we are itching to get back as soon as possible. I can't speak to your destinations in northern Chile as we only visited Torres del Paine (and Punta Arenas area), Chiloe, the Lake District, and Santiago.
As for time, we spent two nights in Torres del Paine and a night in Punta Arenas, three nights in Chiloe, and three nights in the Lake District before heading to Santiago. Of course, it would have been preferable to stay longer in each location but we got a nice overview of each locale. If you're going to do some serious hiking in Torres del Paine you'll need more time there. The Lake District is quite large and you could spend a lot of time there. We visited Puerto Varas, Lago Pueyehue, and Valdivia.
Our mode of transportation was the following: bused into Puerto Natales from Argentina; rented a car for our three days in Torres del Paine; took bus from Puerto Natales to Punta Arenas; flew LanChile from Punta Arenas to Puerto Montt; used a rental car throughout Chiloe and the Lake District; left car in Temuco and took overnight train to Santiago. We didn't use the LanChile Pass but it might be better suited to you seeing as you'll be traveling the full length of the country.
The weather in the Lake District will vary from bright sunny days to pouring rain. It wasn't too cold and we were there the exact time as you will be. Chilean Patagonia will be the same, a bit colder, and very windy. It even snowed a little bit in Torres del Paine, but not enough to stick. The elevation there is very low, similar to the coastal ranges up in British Columbia.
I'll dig around in my pictures and such to give you some more recommendations. Fortunately, we have a few months before you leave.
John in rainy San Diego (Hallelujah!)