The clicking once per turn is probably from the threads of the cap and fork tube already being fully undone, and your continued turning of the cap is having it reaching and falling off the last thread once a turn.
I'm guessing you're doing this with the bike up on a stand, and the weight of the front wheel and front fork, itself, is keeping you from simply removing the cap with your fingers, and that's because the cap is attached to the damper rod that threads into it.
You need to take a look at the Service Manual and read on how the cap is removed on this KYB 46mm inverted open-chamber fork.
Also, while I'm not certain about this for a WR-250R (I'd ask a suspension guy who knows the bike), other bikes I've owned with similar forks had the Service Manual mention any preload adjustment was done by adding thin spacers (they look more like washers because they are not very thick - you may be thinking about old damper rod forks from the 1970s and 1980s) to the bottom of the springs.