Every application will be different, every stove will have it's requirements.. As a general rule: The burn tunnel should be as short as possible. I believe the book says that the burn tunnel should be no more than half as long as the heat riser is tall.. We figured that out pretty quickly. I've seen longer that all that work ok, but I think it's inadvisable. Shorter is better.
The heat riser should be as tall as you can get it within reason. Though it seems that taller than 2 1/2 to 3 feet is unnecessary. It all depends on how well insulated the works are how long the burn tunnel has to be and all that.. Again, I'd say only as long as it needs to be and no more. Too long and you will be loosing heat to the stove, too short and you won't create enough heat to burn all the fuel and provide draft.
The (effective) heat riser height should be measured from the top of the wood feed (air intake), so you will want that as low as possible.