Hi Andy,
firstly, good luck with the Scilly pelagic, I've done pelagics all over the world but never managed to do one out of Scilly.
As for tips for pelagic photography. The camera setup you have is good. I have a 7D with a 100-400 lens, I find the zoom lens a big advantage on the Australian pelagics as many of the Albatross and Giant-petrels come too close for a fixed 300 or 400 mm lens. I think 300 mm is good for the birds you're likely to see.
If your lens has image stabilisation, use option 2, apparently this is better for panning horizontaly. Also, If your lens has an option to change minimal focal lengths, depending on how close the birds are coming it will be worth setting it to the further distance if the birds are not coming within that minimum distance and changing it when the birds come closer.
On your 7D there will be an option in the menue for focus tracking (I think that's what its called) set this to slow, if you are focused on a bird and the bird moves away from your focal spot, on the slow setting the camera won't jump and focus on the backgroud striaght away and hopefully you can get the bird back to your focal point.
On the 7D I like to use the center single point expanded focus option, this is great for small fast moving birds like Prions, Storm-petrels and Pteradroma's where just getting the bird in focus can be tough. If conditions are calm I'll use the central single point focal point, espeicially for larger birds.
I like to stand at the back of the boat where the chumming is going on, this tends to be where the birds come in and hopefully closest to you for photography. On the boats I've been on this is often the steadiest part of the boat. Going upstairs can be good for spotting more birds but there will be more movement up there and photography will be tough.
There are many different waterproofing devices you can buy, I've never used any of them but I always keep a couple of small dry towels in my coat in case of any splashes.
Ask away if you have any questions.
Here's a link to some photos I took on a Wollongong pelagic this year.
http://upload.pbase.com/rob_hynson/wollongong_23_june_2012
cheers,
Rob