After a few more hours of experimentation, I managed to get something decent. I created a file that is run on gnome login that does the following:
The key was to use Accel Profile 6 which feels much more correct for me. If you are having a similar problem, to try to experiment run
xinput set-prop "DualPoint Stick" "Device Accel Profile" 6
xinput set-prop "DualPoint Stick" "Device Accel Velocity Scaling" 10
to see what your input devices are and then use
to see what options you can change. Finally, use
xinput list-props "<device name>"
to set the property.
xinput set-prop "<device name>" "<property name>" <value>