if it smelled then its just not cured rock...its not dead. If you add cured rock, you wont see much of a cycle, if any at all, but if you have uncured rock, you will certainly see the amonia and everything go up and then eventually come back down. As long as it's LIVE you should be fine. so i wouldnt worry about that. You can cure the rock yourself, but since the tank is still cycling i'd just leave it in there.
the smelly stuff is all the die-off on the rock...when you cure it, you're basically getting rid of all the die off. With all the die off now in your tank, you should see more of a cycle now.
oh, and did you brush/rub/whatever all the brown gunk off of it, if there was any? | 
