1. Is Magnus really mehrunes dagon or a aspect of dagon? or the other way around? by the way dagon acts, i just don't see how magnus could be dagon, he seems too mysterious and cool. And isn't magnus the god of magic while dagon is a me smash kinda guy?
2. Do you think akulakhan or numidium are completely destroyed? is there a chance that pieces of them are still around somewhere?
3. Is sotha sil really dead? maybe theres a chance he avoided azura's wrath by transferring his soul into his machine.

1. No, Magnus is the architect of Nirn who left before it was completed, so he is neither Daedra nor Aedra. Dagon was formerly the leaper Demon King, forced by Alduin in his World-Eater form into destroying enough of the kalpa for him to be able to eat it all, and then they both got screwed when history was rewritten to include Akatosh.
2. Maybe. Numidium is more likely to have bits and pieces surviving, as Akulakhan fell into the lava in the very pit of red Mountain, and then the mountain blew up a decade or so later.
3. While his body is dead, none know just what happened to his soul and consciousness. It is possible that he is himself uploaded magically to the Clockwork City and has achieved true trancendence, but that is just speculation and I couldn't possibly comment.

Can you quote where you get this information from about Alduin forcing Dagon? I would really like to know what in-game source you derived this from as it seems a little off to me.

http://www.imperial-library.info/content/fight-one-eating-birth-dagon The Eating-Birth of Dagon. Aside from being the best pre-Skyrim source on the nature of Alduin, it's just a plain good read.