Front brake clicking noise

[clanky]

I've noticed that my front brakes make a clicking noise every time I engage them.  Looking at how the pads are held it looked to me like possibly the pin boots were worn internally allowing the pins to touch the housing wall.  I put new boots on (the old ones looked fine but since I already had the new ones I just replaced them)
Changing the pin boots did not help.
I noticed that the pins are also not cylindrical but rather have flats machined onto them.  Since I have never replaced the pins I did not mess with them and whatever angle they are at was set at the factory.
Any tips or hints would be appreciated.
98 Standard, 202,000 miles
Clanky

[Chrisj CMA]

If you removed and re installed the front wheel it's common to get the clutch side fork misaligned on the axle casing a rub with the rotor rivets and the caliper. If the end of the axle is protruding even a little bit (not flush) that's the problem

If you installed organic pads they tend to make a muffled ticking sound when the brakes are applied. I'm not sure if it reduces over time or you get used to it.

[The emperor has no clothes]

The free floating front brake discs will click normally when applying the brakes. If it's just the initial click, then that's normal. If they click, click, click then what ChrisJ said would be a good starting point.

[Jims99]

Also the drilled rotors cause that noise. Both of my valkyries and my v star do it. Almost sounds like a cicada.

[clanky]

Thanks guys. I  will investigate your responses!