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Do it as a pop up (user initiated) and as the user clicks through the tour, change the window.opener to match the section of your tour while keeping the popup focused. Then the person can "get off the tourbus" at any point and they are there in the section they want.
Your biggest challenge is to combat people's prejudice of all the other useless tours that they have taken in their life, both online and off.
I kind of like the popup idea, except for that i actually don't like popups. But we will consider it, since it seems pretty useful for a guided tour.
Maintance is certainly a main raison, why we tend to use html...
Has anybody any other experiences/ideas?