Enough of the chest beating and name calling! I mean, I'm reading this and could care less. It boils down to this - a healthy, vigorous growing plant is not gonna be prone to damping-off, rots and such, having said that......
I discovered root rot too late in the game and now have a problem.
And my gut feeling is your problem is gonna remain, if indeed it is pythium. I'd get rid of the infected plant material, sterilize all of your equipment and write it off as a bad experience.
My experience with such rots is they're too quick to spread for the typical grower to react soon enough. When that "aw shit" hits, it's over jack. One solution is to try a systemic fungicide like 3336WP, which I don't know if you can get your hands on. I buy it commercially.
http://www.clearychemical.com/support/label/4151SL.pdf
You can find the active ingredient (Thiophanate methyl (dimethyl 4,4’-o-phenylenebis[3- thioallophanate]) packaged for the typical consumer under certain products. It's a super BROAD spectrum fungicide, kicks ass of about anything that can give you problems. It can be used as a soil drench, spray, or dip. It's labeled for turf and ornamentals under some labels, grapes and other consumables on others. The labeling laws are confusing and weird.
And yes, like others have said, prevention is the best cure.
Good luck,
UB