Intermittent clicking noise when shifting in lower gears (1-3). on 1998 Honda Civic

Noise comes and goes. Loudest in lower gears and in downshifting. Once it starts, it can be heard when shifted to neutral, but stops once clutch is depressed. Often clicking noise can be stopped by depressing clutch and re-engaging gear. Clicking is not loud. Does not sound like a mechanical grinding or rubbing.

Asked by for the 1998 Honda Civic
either the flywheel and clutch related alignment, its hard to point out the problem without looking the car.