I think the trust issue goes further than just an atribute on the assebly. I was able to add this line to the version target in the build script: <attribute asis="true" type="AllowPartiallyTrustedCallersAttribute" /> Along with an import statement of: <import namespace="System.Security" /> in order to build the CommonAssembly.cs file.
I was able to update my project with the newly created dll and managed to get past the generic security exception only to be greeted with the following below.
[SecurityException: Request for the permission of type 'System.Security.Permissions.FileIOPermission, mscorlib, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089' failed.]
System.Security.CodeAccessSecurityEngine.Check(Object demand, StackCrawlMark& stackMark, Boolean isPermSet) +0
System.Security.CodeAccessPermission.Demand() +59
System.IO.Directory.GetCurrentDirectory() +182
System.Reflection.Emit.AssemblyBuilderData..ctor(Assembly assembly, String strAssemblyName, AssemblyBuilderAccess access, String dir) +1698440
System.AppDomain.InternalDefineDynamicAssembly(AssemblyName name, AssemblyBuilderAccess access, String dir, Evidence evidence, PermissionSet requiredPermissions, PermissionSet optionalPermissions, PermissionSet refusedPermissions, StackCrawlMark& stackMark, IEnumerable`1 unsafeAssemblyAttributes) +327
System.AppDomain.DefineDynamicAssembly(AssemblyName name, AssemblyBuilderAccess access) +38
StructureMap.Emitting.DynamicAssembly.Init() +184
StructureMap.Emitting.InstanceBuilderAssembly..ctor(IEnumerable`1 plugins) +141
StructureMap.Graph.PluginCache.createAndStoreBuilders(IEnumerable`1 plugins) +146
StructureMap.Graph.PluginCache.Compile() +125
StructureMap.Container.construct(PluginGraph pluginGraph) +118
StructureMap.Container..ctor(PluginGraph pluginGraph) +5
StructureMap.ObjectFactory.Initialize(Action`1 action) +130
PertNear.WWW.Bootstrapper.ConfigureStructureMap() +82
PertNear.WWW.Global.Application_Start(Object sender, EventArgs e) +46