Sounds like you got it figured out man! The stem rot was due to me not turning off the AG water pump after my roots were pretty well in the water. This is due to the sponges staying "too" wet all the time, which water and light makes mold, which caused my stem rot. As long as you take the proper measures, it can be removed, but prevention is the key.
When you start up a thread, send me a link. I'll stop by from time to time to check up and make sure everything is rolling smoothly.
Peace.