I get a loud clicking noise when I disengage the clutch in first gear or sometimes second or third. Any ideas? It doesnt happen everytime.

sounds like it is coming from underneath the car.

I assume manual transmission?

My guess is the clutch slave cylinder can be making the noise when it engages and disenages the clutch release fork. There is some play in that connection but it may be worth a inspection to see if anything is wrong.

If my engine is off and it's quiet, sitting in the garage with the door open, I can hear it engage and disenage. But it is not loud enough to hear once the motor is running.

mine does the same thing im due in next week for the clutch master cylinder replacement and 3rd gear tsb.