Build Run Failing

So everything I have runs fine in the editor, but when I use Build or Build Run it loads the scene but never runs any scripts. I am also getting warnings that say:

“Assets/Plugins/FolderName/ScriptName2.cs(7,9): warning CS0436: The type ScriptName' conflicts with the imported type ScriptName’. Ignoring the imported type definition”

Any help would be great, or a redirection if someone else has had this problem. I couldn’t find one in the search.

Thanks!

It seems like it is building in the wrong order, or I am having circular includes.

So I guess my question is, how can I get rid of circular includes? My hierarchy is pretty intertwined (which is what got me into this mess) so it is really hard to pull stuff apart to get rid of them. Is there a way to get rid of them or do I completely need to rework my hierarchy?