Some thoughts...
Inscriptions of the Nile, where the unspeakable eldrich horror hide:
-A simple man: hideous toad and hairy bat (1)
Simple man = daniel
hideous toad = grunt (looks like a toad? D
hairy bat = brute (its arm)
-Dweller of the sky: mother in sea (1)
Tin hanan (note in archives describes tin hanan as the mother of us all...)
-Give your eye and bowl: mass far below, creator of life (1)
-Fibonacci digger: at graveyard, in gallery (2+4)
-Temptation's tongue fell off at hole: plateau of the octo-leg (1)
-The weights are in equilibrium: the gate (1+6)
Maybe referring to the machine room puzzle? (cistern)
-Feather walker gaze at meal: unstoppable and shapeless (1)
-Dual hooks and beams: many forms seek followers (8+9)
-Two more remain in plain sight.
And those numbers... well there are 9 clues... and if you have them in sequence with adding the numbers
111617117
Without
11124116189
...