Great concepts but many loose ends.

[Bridge]

You see the shadow all the time, right from the beginning. It's the red stuff coming out of the walls. (or at least that's it's physical representation...sort of)

Also the red mist that chases you - possibly the red mist in the Choir as well.

Also, the chemistry is only iffy because the developers decided to have more than one chemical you need to acquire. Royal water alone would have dissolved the tissue (it can dissolve gold after all), so the other chemicals do nothing but make it more corrosive (if anything at all). The in-story explanation for this could be that the Shadow, being a supernatural entity, can withstand corrosion more effectively or can block it somehow. Anyway, if it's just regular tissue, aqua regia would have totally dissolved it.