As a starting point, obtain a dowel which has a cross-sectional area half that of your basic pipe and then by sanding/grinding/whittling/etc. shape it to change the bore volume into whatever configuration you want. The one nice thing about this approach is that you can remove the taper, work on it, reinsert and test your addition or subtraction in a fast, easy and straightforward manner. No more peering down the drain pipe and working like a surgeon, wielding strange homemade tools and waiting for things to dry/harden. About the only trick may be how you affix the taper inside your flute. Because there are holes on opposite side of the flute, the taper will likely have to go either in the center (supported by a wire bracket) or screwed on a side-wall as seen below.

Using this method you can create, test and finalize tapers in a couple hours. It's ideal for those 'what if' moments and you can try out about anything you can imagine. Tapers don't need to have any particular cross-sectional shape, they can be square, round, oval, half-round, rectangular---about anything you desire and find easy to work with.

Removable tapers would add a new and interesting dimension to the shakuhachi.