Hi Evan,
From the symptoms you have described, I would think that you have a problem with the clutch friction plate. Either the disc is loose on the splined hub or the hub is excessively worn on the six splines that provide the drive to the gearbox. You will find that the splines on the gearbox input shaft are longer than the splines in the clutch hub. If the clutch plate is truly centred on the splines, any wear leaves a lip either side of the plate - preventing the plate from floating free when the clutch is lifted. The crankshaft in postwar Douglas engines is located by the front main bearing - causing the rear main bearing to move in the crankcase as the engine warms up. The clunk you heard could also have been caused by the crank moving back under the pressure of the clutch springs - but don't worry about it, this is normal.
If you do have to separate the engine and gearbox, you may be lucky and be able to remove the six 5/16"BSF nuts that retain the pressure plate. With these removed, you can take off the pressure plate which in turn frees the friction plate - if not, you will need to remove the whole flywheel assembly
If the splines are excessively worn, you will need a new clutch friction plate and a new splined adaptor for the gearbox - these are available to LDMCC members through the spares scheme. When removing the pressure plate, be careful, there may be 1/16" thick spacers on each of the six studs.
Regards,
Eddie.