Finding the Problematic dll in "Extracting Referenced dlls Failed" (Unity5)

We are starting to update to Unity5. After upgrading from 4.5.2f1 to 5 we have started to have a problem making builds. Our scenes / projects work correctly in Play Mode. However when we build any scene (including no scene / blank scene) we get the following errors.

 NullReferenceException: Object reference not set to an instance of an object
 UnityEditor.Modules.DefaultPluginImporterExtension+<GetCompatiblePlugins>c__AnonStorey63.<>m__E6 (UnityEditor.PluginImporter imp) (at C:/buildslave/unity/build/Editor/Mono/Modules/DefaultPluginImporterExtension.cs:133)
 System.Linq.Enumerable+<CreateWhereIterator>c__Iterator1D`1[UnityEditor.PluginImporter].MoveNext ()
 System.Collections.Generic.List`1[UnityEditor.PluginImporter].AddEnumerable (IEnumerable`1 enumerable) (at /Users/builduser/buildslave/mono-runtime-and-classlibs/build/mcs/class/corlib/System.Collections.Generic/List.cs:128)
 System.Collections.Generic.List`1[UnityEditor.PluginImporter]..ctor (IEnumerable`1 collection) (at /Users/builduser/buildslave/mono-runtime-and-classlibs/build/mcs/class/corlib/System.Collections.Generic/List.cs:65)
 System.Linq.Enumerable.ToArray[PluginImporter] (IEnumerable`1 source)
 UnityEditor.Modules.DefaultPluginImporterExtension.GetCompatiblePlugins (System.String buildTargetName) (at C:/buildslave/unity/build/Editor/Mono/Modules/DefaultPluginImporterExtension.cs:133)
 UnityEditor.Modules.DefaultPluginImporterExtension.CheckFileCollisions (System.String buildTargetName) (at C:/buildslave/unity/build/Editor/Mono/Modules/DefaultPluginImporterExtension.cs:157)
 UnityEditorInternal.PluginsHelper.CheckFileCollisions (BuildTarget buildTarget) (at C:/buildslave/unity/build/Editor/Mono/Plugins/PluginsHelper.cs:25)
 UnityEditor.HostView:OnGUI()
 
 NullReferenceException: Object reference not set to an instance of an object
 UnityEditor.PluginImporter+<GetImporters>c__AnonStoreyD.<>m__E (UnityEditor.PluginImporter imp) (at C:/buildslave/unity/build/artifacts/generated/common/editor/PluginImporterBindings.gen.cs:104)
 System.Linq.Enumerable+<CreateWhereIterator>c__Iterator1D`1[UnityEditor.PluginImporter].MoveNext ()
 System.Collections.Generic.List`1[UnityEditor.PluginImporter].AddEnumerable (IEnumerable`1 enumerable) (at /Users/builduser/buildslave/mono-runtime-and-classlibs/build/mcs/class/corlib/System.Collections.Generic/List.cs:128)
 System.Collections.Generic.List`1[UnityEditor.PluginImporter]..ctor (IEnumerable`1 collection) (at /Users/builduser/buildslave/mono-runtime-and-classlibs/build/mcs/class/corlib/System.Collections.Generic/List.cs:65)
 System.Linq.Enumerable.ToArray[PluginImporter] (IEnumerable`1 source)
 UnityEditor.PluginImporter.GetImporters (System.String platformName) (at C:/buildslave/unity/build/artifacts/generated/common/editor/PluginImporterBindings.gen.cs:103)
 UnityEditor.PluginImporter.GetImporters (BuildTarget platform) (at C:/buildslave/unity/build/artifacts/generated/common/editor/PluginImporterBindings.gen.cs:111)
 UnityEditor.AssemblyHelper.AddReferencedAssembliesRecurse (System.String assemblyPath, System.Collections.Generic.List`1 alreadyFoundAssemblies, System.String[] allAssemblyPaths, System.String[] foldersToSearch, System.Collections.Generic.Dictionary`2 cache, BuildTarget target) (at C:/buildslave/unity/build/Editor/Mono/AssemblyHelper.cs:129)
 UnityEditor.AssemblyHelper.FindAssembliesReferencedBy (System.String[] paths, System.String[] foldersToSearch, BuildTarget target) (at C:/buildslave/unity/build/Editor/Mono/AssemblyHelper.cs:198)
 UnityEditor.HostView:OnGUI()
 
 Error building Player: Extracting referenced dlls failed.

I've been researching the problem and have seen a number of solutions:

• Changing API Optimization to 2.0 instead of 2.0 subset

• Restarting Unity and/or computer

• Not entering play mode and simply building

Each of these solutions (and some others) have been tried and do not help.

I know from my research that the issue is an out of date or problematic dll or plugin somewhere in our assets. We confirmed this by removing all non-script assets and tried to build. This was successful.

My question is how can I learn which dll etc. is the problematic one? Most other posts of this kind have messages that state the exact dll that is the problem. The above is all the output I have. I have also tried looking in the Unity Editor Log and haven't found anything more helpful in there either.

We have tried to build with both WEBGL and Standalone and this issue occurs in both.