...yeah man Dr Kynes isn't saying not to use the rockwool, he's just saying that when you put the rooted rockwool cube into your net pots that you completely bury them under your hydroton or, in his case, the perlite, ...burying the hydroton makes your plant more stable in the pot and it prevents the growth of algae on the rockwool.
...and i'd not recommend you try and move them now, it sounds like the rootsystem is too well established for you to be able to safely remove them to reposition the rockwool, ...no, i think you need to leave them as they are and just cover them with something, ...you can get covers at a grow shop but you can also use those small styrofoam plates from the supermarket that you'd use for birthday cake and such, just cut a small hole in the center and a slit to slide them over the stem.
peace, bozo