Canadian customs up there is pretty mellow. I crossed on the ferry 5 years ago from Clayton to Wolfe Island with my folding kayak in it's backpack and the agents passed me through in about 5 minutes. Given the choice, I would always rather deal with them than US customs -- the northerners are much more humane and rational. Of course you still have to come back through US customs but if you check with them before leaving to find out what will make your return easier it could speed things up. Are you leaving from Clayton?
My friend up there is an expert kayaker and long time member and outing leader for the Cataraqui Canoe (and kayak) club in Kingston and he knows those waters well. I could contact him and see if he would be open to communicating with you via email (he's retired and travels a lot so I will have to find out if he is reachable at the moment.)
You could also check the CCC's site and links and get in touch with them yourself. Great bunch of folks and excellent paddlers. I did a leisurely tour on the Rideau Canal with them on that trip. Frontenac Outfitters up there would also be a good source of information (there is an ad and link in the CCC newletter for them).
Wolfe Island is cool -- my first trip across the island was the week they were commissioning the last of the windmills that have been installed there.
The Kayak Wing
Free Standing Boat Racks