1) Prepare a calibration to use with v-tune by enlarging as much as possible the area of the fuel table to run in closed loop.
2) Record v-tune data while riding as deliberately as possible. As few sudden/quick throttle changes as you can. Try to operate the engine smoothly in more areas than you normally would.
3) Use the v-tune software to generate a new calibration from the one used while last collecting data.
4) Repeat until you have covered as much of the operational range of the engine as you can and with minimal VE changes from the previous iteration.
5) Restore the fuel tables and other things you'd altered from the base calibration for purposes of v-tuning, keeping the new VE values generated in the process.
6) Log spark data with this new calibration and if spark knock is detected then address the spark timing tables accordingly.
7) If you made changes to the spark tables, perform another v-tune session covering the areas you changed timing so as to get the VEs corrected to match the new timing in those areas.
8) Blend the VE tables as necessary outside the areas you got them "fixed" by v-tuning.
9) Enjoy the fruits of your time and labor.
If your VE tables wind up showing choppy graphs, play around with the EGR settings followed by v-tune runs in those areas. The VE table graphs can have a non-flat shape but you want the contours to flow smoothly with as few and small peaks and dips as possible, but don't adjust them smoother by hand!