No need to take out the rocks.. You haven't added any sand yet??
Well if you are going to add sand to the tank, you will need to either add Live Sand, or dead sand and wait a while for a possible min-cycle to occur over again... It's always best to addd the sandbed and rocks DURING a cycle.. Unless there is a new method that came across this board that I missed out on...
DOn't clean anything, don't siphon any detritus.. Let it all be. I would purchase a good amount of Southdown sand, and then seed it with live sand.. You may get another spike and get a little mini-cycle.. but it shouldn't take long...
Good luck!
Cheers,
Elvis