Scott - If your Guide is AA-grade, it should have mahogany trim (seat frames, thwarts, inwales and outwales, and decks). You can find out by posting your serial number on these forums, which should turn up your original Old Town build record. It sounds like your seat frames just need a good cleaning/bleaching. As Howie suggested, use a good 2-part cleaner and bleach process. Good ones can be found in small quantities at marine shops like West Marine. Some instructions say not to use on mahogany, but in my experience they work great on mahogany. I believe the reason they say this is that these solutions will remove old filler stain.
As for filler stains, I personally avoid them at all costs (no offense intended, Jan... just my preference). To my eye, filler stains simply muddy up what would otherwise be beautiful wood, but this material is the norm in much of the runabout world. If you strip the old finish, clean and bleach according to package instructions, and then sand and finish with a good marine varnish, you'll likely be extremely pleased with your results (but like Howie said, don't use household bleach - very different!). Old mahogany treated this way has a spectacularly beautiful patina that simply cannot be matched by any stain. As for grain filling, if you wish to talk more about that, there are good answers there too that don't involve muddy fillers.
See attachments for one of many examples of mahogany I've treated this way, all with excellent results. First image shows a deck that has been stripped, cleaned and bleached. Originally the mahogany was very dark and ugly. Second image shows the same deck along with the original trim (caps) with a number of coats of varnish. No stain of any kind, only varnish.
Michael
