I have used the rapid rooter method but you should cut a half inch or so off the top of the rooter cube or you will have trouble with the collar pushing up. I suggest you put the rooter cube in the netpot then mark and cut before putting the seed in. No root issues starting with the rooter cubes either at least I have never had an issue with it.
I don't think I've used a gallon or 2 of bleach in all my life. Laundry included lolI've been using the same ez clone style sprayers for over a year, after every run I dump a gallon or 2 of bleach into the 20 gallon res full with water and let it run at least over night, idk if that is why I haven't experienced the clogging issue?