i belive that the shards have to be represented as bodies of water, thats what the first "hero of ages" saw on his way up north to terris (i totaly blanked on his name), its what filled the well of assention, and was outside of elantris.
if we take that the pools of water are the physical manifistation of shards, i think we might be able to extrapolate that the source of the pits is infact a pool of water, but due to the nature of the pits, it goes through a geological process that turns it into the geods and atium. (i think of it as the water is leaching through the rocks and when it finds a pocket it creats a geod the same way a clam would make a pearl).
This could also tie into the flowers that make such vivid colors in warbreaker. the plants feed off the shard lake and are able to create such wonderful dies.
lastly, as far as Elantris goes, it seems to me that the Dakhor dont use Aeons, Raodin describes the bones as having intricate patterns, not recognizable Aeons (and i think that he could recognize them having become an expert in a few short weeks).
I still think Jaddeth is a shard, but there isnt much proof. however i can imagine a senario as such:
Everything on (insert planet name here) is going along just fine, then Adonalsium gets broken up into his shards and they pierce through time and space and these shards endup on diffrent planets. Poor (insert planet name here) gets hit with two shards. This causes a rift in theological doctrine those that follow Shu-Korath go with the shard in elantris and shu-dereth goes with the shard that i believe is under a mountain somewhere.
also, i think it would make sense for the shards to travel in "pairs" either because they are spiritualy bound to eachother as oposit forces or because as they go from wherever Adonalsium is into our real, the shards fracture again into two parts.
so all this is very detailed and as i have seen from other fandoms, the more detailed the theory the more likely it is to be WAY off.
please destroy it apropriatly