Very enjoyable read and wish you all the best luck in figuring out the mystery. I am going to put down some of the general thoughts i had throughout this read if i can remember them all. They are not meant to be an insult just some thoughts that ran across my mind during this quest.
1. This cavern was obviously created by tons of water flowing through it of a long time. Anything ancient would more than likely be washed out of the cave into the low areas outside i would think. The area after your "artisian well" that curves around and you said there seems to be a man made looking tunnel but the side near the well is blocked off, this could be somebody blocking it off on purpose for some reason and reminds me of the natural flow of a river eroding land and creating
Oxbow Lakes.
2. The "mud stone" reminds me of a wall at Meramac Caverns when i was a kid, it was a rock wall but i forget why it was tacky, mud-like, and people used to toss coins at it just to make them stick. Is the "mud stone" just pure mud stacked up in that shape without being ever washed out after big rains? or possibly stone that has a layer of softness to its outside. Also with the stone my initial thought of a stone with markings on it would be to signify a grave marker AND was it meant to stand upright like a headstone and fell maybe causing the top to crack off. With the "Mud stone" you could possible try some digital scans or something or take a mold and take to a university to do a digital scan and may get all of the missing pieces, or do oldschool kid stuff and put paper on it and rub with charcoal or something to get an impression. Is the stone also partially buried in other mud and maybe missing out on some of the symbols?
3. Lighting... Well i had several thoughts on this, I used to be an insurance adjuster and noticed that a digital camera with the flash on in complete darkness can highlight or capture water spots and other things that i couldn't see with my naked eyes, not sure if that would help in the cave or not. Also Blacklights and UV lights with a video camera can be utilized and some minerals/rocks will glow/flouresce.
4. I would think NEVER fire off a gun in a cave if you were thinking of taking one. It could cause a cave in from the shot echoing throughout the cave, much like the difference between a blackcat firework on your palm vs. one in a closed fist.
5. Be careful not only of the animals but their droppings, i have heard bat droppings and others can make a person VERY sick and cause death, unsure though. Even the Ammonia content can't be good if there is an area of a lot of it from bats.
GL in your adventures and hope you find what you are looking for