You are on the right track - When you test for chlorine the first number is Free chlorine, the second number is combined chlorine, the total chlorine is adding fc to cc. So I don't know where you are getting the .5 - sometimes if you wait a while after adding the drops to test for cc, the water turns slightly pink - this isn't cc. You just want the results of when you first put in the 5 drops. You do need to get cya in the water - put half of what it says to put in on the bottle. You can always bump it up later, and the only way to get rid of it is by draining water. Shoot for 30 - 50, it can take a week for it to show up in a test. You can put it in the skimmer or put it in a sock and tie it near a return jet. You will also want to move your calcium up to 200 - 400. This is necessary in a gunite pool.

As for the stains - they may be organic, which will come off when you get some high chlorine in the water. If they didn't come off with Vitamin C, then my guess would be they are organic. You can also try a pumice stone, or something that will rub a little harder on the gunite. They sell a stain eraser at the pool stores that is good. It can clip on the bottom of a skimmer pole. It rubs the stain off, like a gentle pumice stone. Or you can just bring your clorine level up high and it will fade them in time.

Hope this helps, feel free to ask any questions you may have.