Hey Oly,
We have shared a bunch of this on Twitter @theoutdoorline and facebook as well as on these pages and I'm more than happy to share the info here as well!
As I write this I'm working on my annual Sitka blog but we do indeed ship the boat up on Alaska Marine Lines and it rides to Alaska way up high atop a barge!
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The boat arrives in about a week and then we fly in on Alaska Airlines.
As far as the costs, you'll have to contact Alaska Marine Lines for your cost per foot and we stay at the Sitka Super 8 which is close to another nice hotel, the Westmark Sitka.
We've got a regular group of guys that share the costs but if you don't want to go to that extent, there are several great charter services in Sitka that will be happy to show you the ropes!
Try Derek Floyd at Reel Class Charters, Eric Linde at Horizon West Charters, Seth Bone & Don Orrell at Kingfisher Charters and Greg Kain at Kain's Fishing Adventures!