For adjusting the octave balance with a cylindrical bore, take a look at this thread:
viewtopic.php?f=1&t=108141. That is probably the easiest solution to your problem.
If you want to use a conical bore, not just any cone will do; it has to have the right taper to balance the octaves.
For tuning calculators, WIDesigner is the only one I'm aware of that explicitly takes both octaves, and bore profile, into account:
https://github.com/edwardkort/WWIDesigner/wiki.
I have heard that you can tweak the octave balance for individual notes by undercutting toneholes on the upstream or downstream edge, but I have not tried this myself.