Any ideas? I have a noise, a loud squeak coming from my 99 FXSTC. It only happens when I am shifting to the next gear, up or down. As soon as the clutch take hold I hear a short loud squeak, if I am coasting down a hill and letting the motor slow the bike down I hear it. It’s hard to tell where is coming from but definitely from the area of the engine and I believe from the left side.

 

Is it just one squeak or a constant squeaking when it happens?
As you slow down, sounds like it could be a tight belt problem. Try spraying the belt with some silicone on the inside (tooth side) and see if it changes it.

Also check the pivot shaft for the shifter ( a common problem) it probably needs greasing. You can also install a grease fitting in the boss by drilling and taping it , then install the grease fitting.