Well, since we don't definitively know what the problem was - black algae, metal stains, or something different - it is possible that the low FC levels let some algae take hold. The other alternative is that when you let your Ph get so high, some of the metals in your water could have leached out and into the plaster. If these stains reappear, do a quick check with a vitamin C tablet (just rub it on the black spot) to see if it goes away. If it does, then iron metal is the likely culprit. If there is no change, rub a chlorine puck on it. If that gets rid of it, it's probably algae related. Lastly, if none of those work, there's a good chance that it's copper staining. There's no way any of us here can tell you the definitive cause without you doing some checking of these various possibilities.
A good CSI number does not mean your water is in good shape from a sanitizing or metal standpoint. It has more to do with calcium scaling. When your CSI is out of range, it can cause the plaster to deteriorate. An unbalanced Ph is the fastest way to get your CSI way out of whack, which you did have several times during your test. It looks to me like there were times when your Ph was too high or low for a week at a time. You should absolutely pay more attention to this.
It sounds like you are putting too much importance on the CSI reading. To me, is more important to take care of the FC, Ph, etc. If you keep all of those things in line, the CSI will take care of itself. Each component is as important as the next.
