if your doing a overhaul of the tank then either way your probably going to see some whether you deal with it now or you set your tank up again....if theres dieoff cyano can appear.so if you left your rocks to just soak for weeks whatever died in that process is feuling your outbreak.to stop the outbreak you need to get your system stabiled sooo what you want to do is remove all your rock and in extra ro water dont be afraid to give it a thrashing or a scrubbing then place it in the storage bin your going to use with a decent powerhead and a small heater. your gonna have to empty your tank to drill as far as i know so its your call on sand if its to be left in i dont know if you can or cant while drilling.
after you get your plumbing all fixed and filled with new water then you can add your rock back in now your gonna see a cycle no ways around it where you created dieoff. its gonna be a good one by the sounds of it as well so i hope you dont have any fish if so you may want to give thenm to someone to babysit.
if your going to store your rock for a good time then do water changes on it.
once in the tank and your cycle is running your gonna have to keep up with maintanace for water changes lots of flow manual removal and blowing off ditrius.start with a low light cycle of a few hours slowly building up to what you want to do.
keep your nitrates and phosphates at zero its alot easier to do then when they get high, so think about using some of the nitrate and phosphate reducing reactors on the market theres lots to choose from.
get to planning a refugium it will do your system wonders with beneficial life.
run carbon as much as you can i ran carbon in tanks with sumps or without its very usefull in clearing out your water of harmful contaminants.
dont rush it or your gonna get stuck with something youll have to fix in order to work get everything you need together then start your cycle youll find it that much easier
but yes run carbon!!!!!