It appears the errors are coming from the plugin manager. I've made certain to update installedPlugins.txt per the upgrade instructions and removed the old plugin folders.
[FileLoadException: Could not load file or assembly 'Newtonsoft.Json, Version=6.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)]
[FileLoadException: Could not load file or assembly 'Newtonsoft.Json, Version=9.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)]
System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) +0
System.Reflection.RuntimeAssembly.nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) +36
System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) +152
System.Reflection.Assembly.Load(AssemblyName assemblyRef) +36
Nop.Core.Plugins.PluginManager.PerformFileDeploy(FileInfo plug) +169
Nop.Core.Plugins.PluginManager.Initialize() +1327
[Exception: Plugin 'Credit Card'. Could not load file or assembly 'Newtonsoft.Json, Version=9.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)]
Nop.Core.Plugins.PluginManager.Initialize() +2029
[Exception: Plugin 'Credit Card'. Could not load file or assembly 'Newtonsoft.Json, Version=9.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)
Could not load file or assembly 'Newtonsoft.Json, Version=9.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)
Could not load file or assembly 'Newtonsoft.Json, Version=6.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)
]
Nop.Core.Plugins.PluginManager.Initialize() +2437
[InvalidOperationException: The pre-application start initialization method Initialize on type Nop.Core.Plugins.PluginManager threw an exception with the following error message: Plugin 'Credit Card'. Could not load file or assembly 'Newtonsoft.Json, Version=9.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)
Could not load file or assembly 'Newtonsoft.Json, Version=9.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)
Could not load file or assembly 'Newtonsoft.Json, Version=6.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)
.]
System.Web.Compilation.BuildManager.InvokePreStartInitMethodsCore(ICollection`1 methods, Func`1 setHostingEnvironmentCultures) +613
System.Web.Compilation.BuildManager.InvokePreStartInitMethods(ICollection`1 methods) +141
System.Web.Compilation.BuildManager.CallPreStartInitMethods(String preStartInitListPath, Boolean& isRefAssemblyLoaded) +102
System.Web.Compilation.BuildManager.ExecutePreAppStart() +157
System.Web.Hosting.HostingEnvironment.Initialize(ApplicationManager appManager, IApplicationHost appHost, IConfigMapPathFactory configMapPathFactory, HostingEnvironmentParameters hostingParameters, PolicyLevel policyLevel, Exception appDomainCreationException) +531
[HttpException (0x80004005): The pre-application start initialization method Initialize on type Nop.Core.Plugins.PluginManager threw an exception with the following error message: Plugin 'Credit Card'. Could not load file or assembly 'Newtonsoft.Json, Version=9.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)
Could not load file or assembly 'Newtonsoft.Json, Version=9.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)
Could not load file or assembly 'Newtonsoft.Json, Version=6.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)
.]
System.Web.HttpRuntime.FirstRequestInit(HttpContext context) +9946024
System.Web.HttpRuntime.EnsureFirstRequestInit(HttpContext context) +90
System.Web.HttpRuntime.ProcessRequestNotificationPrivate(IIS7WorkerRequest wr, HttpContext context) +261