There is no science to the next part - to align the hole drilling for the LED, I used a straight edge and I aligned it with the + cross-hair (yellow arrow) of where to drill the shaft hole and then drew the line.
Then I got on the bike to see if it was lined up - it wasn't - so I drew the corrected one you see below and proceeded to drill the hole.
If you plan on mouting the controller in the same general area as i did below is shown where the mounting post for the panel is in relation to where you are drilling.
Something to be aware of - consider it a soft caution.
Note - the Side Panel goes for about $780.00 be sure you want to do this.
After you start drilling there is no going back.
Some tips for drilling:
the instructions call out the sizes you need (9/32" for the shaft and 7/64" for the LED) or in metric-speak 7.25mm/2.77mm respectively
Don't start with those - start with smaller pilot holes and work your way up.
Use an electric drill as you have more control on speed (at least I do on mine)
Drill from the finished paint side - this will leave a cleaner hole and minize paint flacking by the outer edges of the drill point
Slow speed, even pressure - if you have sharp bits it will go quick
try to have a drill size that is one level below what is stated in the instructions - you will then be able to gauge how much drill opening you have left.
Last but not least - go slow, evenly and take your time
This shows a ziptie that was added to the panel post support, helping to provide support for the PCB. A 3/16" hole must be drilled in the support for the ziptie. Do NOT overtighten the ziptie!