sounds good, there'd be so much to choose from though. I'd be thinking about maybe launching kyleakin on skye, giving access to loch duich, sound of sleat, and some relatively sheltered channels to explore around raasay, scalpay etc.
Making it an A to B i'm not sure about, I've kayaked from Kinloch Hourn to the head of loch Duich and walked back through the hills to get my car, but finding good slipways would probably be a bit trickier!