As others mentioned, deep clunks are normally associated with main bearing. If that is the source, it is usually accompanied with a drop in oil pressure.
but other clunk sources would be a loose flywheel or a crank pulley with an oversized hole or either not properly installed. also consider any bolt on accessory drives with loose bolts.
Try clutch in or out, air (if you have it) on or off, different engine speeds and loads. Check back with your findings and maybe we can be of more help.
