Cooking Live Rock - Exact Process?

Palys are one of the only things that survived during my process. The rock was completely clean when I reintroduced it to the display, but about 6 months later, some baby palys started showing up. I tweezed them, and I believe I am good now... haven't seen any sign of them for about 9 months now.
 
I have started this process of "cooking" approx 200 lbs of live rock and have some questions.

A little background, I am a novice that "inherited" the duties of caring for a 150 gallon reef tank that my husband totally neglected. It was set up by a professional about 6 years ago with all the "trimmings" (Fluval filter, chiller, Coralife lighting and skimmer, wavemaker, etc) and was initially well-maintained but has had virtually no maintenance in the last year. A few years ago a housesitter closed the door to the tank room and the tank overheated killing most of the corals and fish (chiller could not keep up). It's only surviving inhabitant is a single yellow tang that is set-up in a separate small tank for now. I have started the "cooking" process as the rock was covered in detritus and areas of what looked like dark green or black solid webs of "something". The rock did have a lot of purple coraline. Right now the tank has a brand new layer of 4" of CaribSea Fiji pink sand, all new saltwater, and I have placed some of the rock back in that looked clean (basically void of color except for some coraline). The rest is still "cooking" in tubs with saltwater, circulation and heat.

My dilemma is, I don't know how long the remaining rock needs to be cooking. I am getting very little detritus out of it but a lot of it is an ugly color (slightly green in places but mostly the brownish detritus color). I tested the water that it is in and the ammonia level was 2, nitrites and nitrates 0. The main tank's ph was good, ammonia, nitrites and nitrates 0 so the tank has not cycled yet. So, I am wondering if I should just place the rest of the rock in and perhaps some of the ammonia water to get the cycle started? If I cook the rock too long will it remove beneficial bacteria? Will a cleanup crew help with the discolored rock? I've tried a wire brush to remove the discoloration and it only helps as small particles of rock have broken off to reveal "clean" looking rock. Anyway, thanks for any thoughts or advice on this. I took some pictures but they do not adequately show the coloration of the rock.
 
Cooking rock is kinda false hope imo.

At 8.4 ph calcium carbonate is at max absorption for taking in phosphate, at 8.4 it's around a 90%+ absorption rate. That means it goes in and doesn't come out. If it does come out, at a VERY slow rate.

When taking into consideration flow rates in the tank, that means your rock will absorb more than a gfo reactor. (exposure rates; 2000gph flow in a tank > 250gph through a gfo reactor; even if the reactor absorbs 100% phosphate per pass)

Remember, this is only concerning calcium carbonate rocks.

The best argument I've seen against this is 'bacterial mass will cover the sites in the calcium carbonate and will prevent the phosphate from being absorbed'.
Yet that is nullified by the fact we've all seen precipitate on heaters, which we all know bacteria loves to grow on. Therefore, the bacteria did not prevent the precipitate from achieving adherence to the heater.
 
Questions

Questions

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So basically like 4 months ago, I bought 50lbs or so of LR from a friend of mine that was getting out of the hobby. It came with a couple of hermit crabs, bristle worms and no other pest from what I can see. I got some dry rock from another person who was also getting out of the hobby. Basically for 4 months I have had the rock cooking in buckets with powerheads, heaters and a 100 WATT LIGHT on both buckets and phosphate reactors hooked to one bucket. I also have been testing the water and adding calcium after water changes. Im new to the hobby myself...and the gentlemen helping me is recommending me use lights every day. He is claiming that certain beneficial bacteria or whatever it is comes from providing light everyday. I also have Asterina sea stars here and there...and I added only a COUPLE of snails...one turbo and some other little guys...they all do fine, none of them died and seem to be enjoying themselves. My question is I'm about to set up my tank in a month....should I keep the lights on, or do the total darkness thing? The rocks just sit in the tubs...I do water changes like every 2 weeks, shake of the rocks in a bucket and get all the crap off them yall talk about :). I have a little bit of hair algae but it seems to stay pretty low and its not that much really at all. I guess at first when I came into the hobby I was hoping just to keep the LR "alive" and save money on buying it from a LFS...because I basically got 100lbs for 100 bucks. However...in the recent months I have been reading that from what I think...what I am doing is actually good in 2 ways...its creating good beneficial bacteria, as well as cycling the rock I already had as well as the dry rock I bought. Anyways just your thoughts on things I should tweak the next month or two before adding it to the tank, and also if I need to get rid of the light.
 
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