Hi there,
First off, congratulations!
Generally, kayaking with Orca whales happens in Johnstone Straight, on the East Coast of Vancouver Island. There are pods of resident Orcas up there. While I've been up that way many times (Quadra Island) I've never done the kayak / whales thing. That being said, I've heard good things about this operator -
http://www.kayakingtours.com/
Look at their Johnstone Straight tours.
You need to allow a day to get from Vancouver to Quadra Island. You'll take the Vancouver Island ferry from Horseshoe Bay in West Vancouver to Departure Bay in the (small) city of Nanaimo (pronounced Nan-eye-moe), then drive north to Campbell River. In Campbell River you take another short ferry over to Quadra Island.
http://www.bcferries.com/files/image...routes_map.pdf
While it takes a day, it's a beautiful trip.
It's about a two-hour drive from Nanaimo to Campbell River on the 'inland Island highway 19' or about 2 3/4 hours if you take the much more scenic oceanside highway 19A, which is what I'd recommend.
In terms of your 'Wilderness Resort' both the Sonora and Wickaninnish Inn are on Vancouver Island, so it doesn't make a lot of sense to return to Vancouver for that part- Do your Kayak trip, then stay on the Island and head to the wilderness resort. The Sonora is in the same area you'll be Kayaking, so I'd suggest Wickaninnish instead, as it's on the West Coast of Vancouver Island - You'll see different, more rugged, geography.
To get to the Wickaninnish you'll drive from Campbell River to the village of Tofino. That drive is about five hours - Again, very scenic. I'd use 19, not 19A, for that one, connecting to Highway 4 to head over the island to the west coast.
I would say two days in Tofino would be enough.
You could then return to Vancouver, do the Whistler bit and then fly home.
Post back with your next questions once you've digested that and we can work on your intinerary some more
