Shame to waste that paintwork!
If it were me, I’d consider other options first.
Shave a bit of the cylinder head if that is what is causing the cowling to sit proud. You might be very reluctant to do that!
However, if it isn’t that, use a shorter ‘long’ hexagon nut, or modify existing.
Make, or buy a cowling packer (Scoterotica or Taylor Tuning might make them)