On a side note what is this plugin bypass thing I keep reading about? Also where can I find more mods? the Nexus does not seem to have many of the more popular mods from the standard version. Do I have to find a compatible list and then convert the ones I want myself or...That's only necessary if you are exceding the base limit of 10 mods. You don't need it if that's not the case, same for the Plugins file.
Didn't take a look at the mods you were loading, that shouldn't stop Atmos for reading the mods. But if it worked, then great!