Michael,
Decks can sometimes be difficult to remove without damaing surrounding structure. I've done several very early AA-grade Otcas, all of which had decks installed with steel screws. As much as I wanted to get the iron out of there, they were impossible to remove without damaging the near-perfect wood they were in. Thus I was left with a situation much like yours. I've also had this problem on torpedo-ended courting canoes- even with the decking removed, it's a long way into the ends of the canoe. I agree with Gil- remove the decks- but if this isn't a viable answer...
The solution to stripping is easy- just slosh stripper up in there, and distribute it with some long-handled device. You could duct tape a cheap chip brush to a longer handle, or you could wrap a bit of a rag around the end of a stick. My personal preference is a bottle brush. I use long wire-handled plastic-bristled bottle brushes in the lab every day- they are impervious to most chemical insult including methylene chloride-based strippers, they easily reach the ends of even an Otca (a "real" Otca with decks as in yours), and the bristles do a great job of distributing and cleaning. After the stripper sits a while, I just go back and scrub the ends with the bottle brush to loosen all the gunk, rinse, then scrub out again with concentrated TSP. The plastic bristles are very gentle and the way they are inserted into the wire, there is no danger of metal damaging wood. Results- perfectly clean all the way into the ends and in every nook and cranny.
Michael