I just went thru this process a few weeks ago and I think I posted up most of the pics. I was restarting up a RDWC that had been sitting drained a while, and I failed to drain the chiller or some of the other lines. When I added RO and started pumps by basement smelled like a sewer. I can't imagine what all was growing in there, but it was pretty bad.
Step 1 - clean. With the system topped off with clean water, add H2O2. Run all pumps and air stones. Get into there on your knees with a toilet brush and get every nook and cranny.
Step 2 - flush. As much as needed for your grow style. If you are keeping the H2O2, you just need to get it down low enough for your grow. If running biologics, zero. I use test strips to know.
Step 3 - adjust PH, nutes, add silica or whatever, and then beneficials. If running bennies, give it a week before you
Step 4 - add rooted plants.
As far as level of H2O2, I use a lot. I also use it to clean all surfaces. Floors, walls, pipes, fan blades, etc. As far as where to run your grow, 5-10 PPM seems about right for most people.
I think you can replace the above H2O2 with Chlorine, but I have never done this.