Yes, the TW clunks on downshifts. It can be lessened by learning how much to rev during the downshift. You want to bring the RPMs up to whatever they will be in the next lower gear after releasing the clutch. This will vary somewhat depending on whether you are braking hard on the downshift, going up or down hills, etc. If you do it right there won't be much clunking....it's just a quick little blip.
I always shift into first at a stop, but only at the last few feet because you can skid the rear wheel if you do it at too high of a speed.....Don't ask me how I know this! At stoplights I ALWAYS want to be in first gear because if you are about to get rear-ended you need instantaneous acceleration!