How do I remove the "security" cap over the air screw on a 1980 Yamaha
XS400 so that I can adjust the air to fuel ratio?

I'll bet it comes out like this:

http://www.cartestsoftware.com/fz1/jetkitinstallation.html

Drill Out Mixture Screw Plugs: 

This turned out to be very simple and took just a few minutes. Using
Ivan's supplied drill bit, very light pressure, and a slow drill speed
the brass just falls away. The plug actually just rotates right out as
the bit bites into the brass. No need to use the supplied pull out
screw.