Hmmmmm.......cross your fingers, meditate, pray to whomever you pray to.... Usually from what I've read, stem rot is fatal. I've read that this seems to have one recurring theme, rockwool. It seems that rockwool is awesome for germing because of it's ability to hold moisture---practically forever---but as you've found out, it can be a bad thing for plants once they get older.

I found the same thing with Rapid Rooters, as I mentioned earlier.

For what it's worth, I'm really sorry this happened to ya. Don't give up though. Keep us updated.