I'm a bit unclear about what you're asking, but I think you're trying to match new mahogany parts to the old mahogany in your canoe (in some places, it seems as if you may be asking about staining the hull as well). If the former, here are some suggestions:
First, if you haven't already done so, you might want to use a 2-part teak cleaner/brightener. It can make a big difference in the appearance of you old wood. Since presumably you're taking out some pieces, try this process on some old wood scrap to see how it reacts. Second, be sure you're using the same type of wood for replacement- there are a variety of tree species generically labeled "mahogany" in the lumber trade. Third, attempt to find boards that are similar in figure and color to the old wood in your canoe. Fourth, you'll almost certainly need to mix stains, rather than relying solely on single manufacturer's colors alone. And then, you may need to layer multiple coats, perhaps in different colors.
You might also try different kinds of stains- there are oil-based ones, water-based ones, alcohol-based ones, pigments, dyes... Some are more or less color-fast than others, especially under UV exposure (but you should be using a UV-sheliding varnish over the stain anyway), so read up on them before trying new ones.
Hope this helps!
Michael