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As far as the staining is concerned I think everyone now agrees that it is some kind of stain made by some kind of fluid flowing from the shaft. IMO I don't think it's candle wax for the reasons Romulus gave. The flow pattern.
No idea what it is other than it's a stain and it's been photographed on numerous occasions, over numerous decades, by numerous cameras, and numerous formats, and numerous lighting techniques.
Ori's suggestion is the best, north facing, open shaft, open to torrential rain once every twenty years for a thousand years. That's 50 torrential rainstorms. It's gonna get wet.

I don't believe this. Even torrential rain is not going to cause huge amounts of water flowing through the shaft and create waterfall-like widening stains at the shaft opening wall. Only a small amount of raindrops will get in. Even with 50 torrential rainstorms every time small amounts of rain will enter the shaft. So "it's gonna get wet" but this rain didn't create these stains.