Wait until the clone is REALLY well established...like a month after taking it... keep the top of the rockwool plug as far above the soil surfae as you can... chip away at it carefully with forceps and try to reduce its bulk without damaging the plant... gotta get that moisture trap outta there! A little rockwool left behind isn't going to matter too much but if you can get most of it off you are better off.

I was looking back at this thread too and if the problem wasn't root rot it was plain suffocation. the canoe leaves point to that.