I'm basically in the same boat as you! I purchased 50lb Pukani from BRS. I hand picked off all the dead/loose debri I could see with pliers and scrubbed the rocks with a stiff plastic bristles. I wasn't concerned with starting my bacterial cycle yet since I planned on aquascaping the rocks completely dry first, so I soaked my Pukani in dechlorinated freshwater in a Rubbermaid tub keeping the temperature around 82 degrees and using a couple of powerheads...I did this for about 6 weeks. During that time, I did several water changes...the first week it smelled rough while the debri decayed. I was testing the water routinely to see what was going on with the decay process...ammonia obviously went through the roof. It did start to leach a bunch of phosphates, so I put a bag of Phosguard in the stream path of one of the powerheads and that cleared out the phosphates pretty well when changing the Phosguard about every 4 days. I also regularly scrubbed the rocks with a plastic bristle brush before a water change just to break off any remaining surface junk. After about 6 weeks, the phosphates were leveling off and remaining very low...although still present...so I stopped the cure process and let the rock completely dry out. I'm in the process of playing with the aquascape now.
I think I would do this process again. Some said I could have put this directly into my tank and cured/cycled at the same time, but I'm glad I didn't. From everything I've read, there is going to be a fight with the algae during the cycle anyhow, so hopefully my process has reduced the phosphates present enough to keep that somewhat under control...I'll probably still keep a bag of Phosguard in the sump during the cycle to help control any additional phosphates present. I might as well...my LFS guy sold me a huge container of it...I think I got taken there a little, lol.