[Nexus 5 Android Development] mistersixt:
Wait, maybe I mixed something up: I tried those Gapps-6.0 from dankoman in the meantime, and I think I might have replaced the SetupWizard while trying his Gapps.

So now I did a fresh install, replaced the content of your zip archive via adb/TWRP and bootet up the phone, the pop-up still appears constantly, but the error message is different (again) I think :

10-08 15:25:14.439 740 754 I ActivityManager: Start proc 6678:com.google.android.setupwizard/u0a58 for activity com.google.android.setupwizard/.SetupWizardActivity
10-08 15:25:14.462 6678 6678 W System : ClassLoader referenced unknown path: /system/priv-app/SetupWizard/lib/arm
10-08 15:25:14.465 6678 6678 D AndroidRuntime: Shutting down VM
10-08 15:25:14.466 6678 6678 E AndroidRuntime: FATAL EXCEPTION: main
10-08 15:25:14.466 6678 6678 E AndroidRuntime: Process: com.google.android.setupwizard, PID: 6678
10-08 15:25:14.466 6678 6678 E AndroidRuntime: java.lang.RuntimeException: Unable to instantiate application com.google.android.setupwizard.SetupWizardApplication: java.lang.ClassNotFoundException: Didn't find class "com.google.android.setupwizard.SetupWizardApplication" on path: DexPathList[[zip file "/system/priv-app/SetupWizard/SetupWizard.apk"],nativeLibraryDirectories=[/system/priv-app/SetupWizard/lib/arm, /vendor/lib, /system/lib]]
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at android.app.LoadedApk.makeApplication(LoadedApk.java:578)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at android.app.ActivityThread.handleBindApplication(ActivityThread.java:4680)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at android.app.ActivityThread.-wrap1(ActivityThread.java)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at android.app.ActivityThread$H.handleMessage(ActivityThread.java:1405)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at android.os.Handler.dispatchMessage(Handler.java:102)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at android.os.Looper.loop(Looper.java:148)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at android.app.ActivityThread.main(ActivityThread.java:5417)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at java.lang.reflect.Method.invoke(Native Method)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at com.android.internal.os.ZygoteInit$MethodAndArgsCaller.run(ZygoteInit.java:726)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at com.android.internal.os.ZygoteInit.main(ZygoteInit.java:616)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: Caused by: java.lang.ClassNotFoundException: Didn't find class "com.google.android.setupwizard.SetupWizardApplication" on path: DexPathList[[zip file "/system/priv-app/SetupWizard/SetupWizard.apk"],nativeLibraryDirectories=[/system/priv-app/SetupWizard/lib/arm, /vendor/lib, /system/lib]]
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at dalvik.system.BaseDexClassLoader.findClass(BaseDexClassLoader.java:56)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at java.lang.ClassLoader.loadClass(ClassLoader.java:511)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at java.lang.ClassLoader.loadClass(ClassLoader.java:469)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at android.app.Instrumentation.newApplication(Instrumentation.java:981)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at android.app.LoadedApk.makeApplication(LoadedApk.java:573)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: ... 9 more
10-08 15:25:14.466 6678 6678 E AndroidRuntime: Suppressed: java.io.IOException: No original dex files found for dex location /system/priv-app/SetupWizard/SetupWizard.apk
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at dalvik.system.DexFile.openDexFileNative(Native Method)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at dalvik.system.DexFile.openDexFile(DexFile.java:295)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at dalvik.system.DexFile.<init>(DexFile.java:80)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at dalvik.system.DexFile.<init>(DexFile.java:59)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at dalvik.system.DexPathList.loadDexFile(DexPathList.java:279)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at dalvik.system.DexPathList.makePathElements(DexPathList.java:248)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at dalvik.system.DexPathList.<init>(DexPathList.java:120)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at dalvik.system.BaseDexClassLoader.<init>(BaseDexClassLoader.java:48)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at dalvik.system.PathClassLoader.<init>(PathClassLoader.java:65)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at android.app.ApplicationLoaders.getClassLoader(ApplicationLoaders.java:58)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at android.app.LoadedApk.getClassLoader(LoadedApk.java:376)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at android.app.LoadedApk.makeApplication(LoadedApk.java:568)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: ... 9 more
10-08 15:25:14.466 6678 6678 E AndroidRuntime: Suppressed: java.lang.ClassNotFoundException: com.google.android.setupwizard.SetupWizardApplication
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at java.lang.Class.classForName(Native Method)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at java.lang.BootClassLoader.findClass(ClassLoader.java:781)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at java.lang.BootClassLoader.loadClass(ClassLoader.java:841)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: at java.lang.ClassLoader.loadClass(ClassLoader.java:504)
10-08 15:25:14.466 6678 6678 E AndroidRuntime: ... 12 more
10-08 15:25:14.466 6678 6678 E AndroidRuntime: Caused by: java.lang.NoClassDefFoundError: Class not found using the boot class loader; no stack trace available
10-08 15:25:14.467 740 1827 W ActivityManager: Force finishing activity com.google.android.setupwizard/.SetupWizardActivity

---------- Post added at 03:41 PM ---------- Previous post was at 03:26 PM ----------

First the logcat was showing that a lib was being search in /system/priv-app/SetupWizard/lib/ ... while your zip content was showing "oat", so I changed the directory, and I now get this:

10-08 15:36:55.272 2973 2973 D AndroidRuntime: Shutting down VM
10-08 15:36:55.273 2973 2973 E AndroidRuntime: FATAL EXCEPTION: main
10-08 15:36:55.273 2973 2973 E AndroidRuntime: Process: com.google.android.setupwizard, PID: 2973
10-08 15:36:55.273 2973 2973 E AndroidRuntime: java.lang.RuntimeException: Unable to instantiate application com.google.android.setupwizard.SetupWizardApplication: java.lang.ClassNotFoundException: Didn't find class "com.google.android.setupwizard.SetupWizardApplication" on path: DexPathList[[zip file "/system/priv-app/SetupWizard/SetupWizard.apk"],nativeLibraryDirectories=[/system/priv-app/SetupWizard/lib/arm, /system/priv-app/SetupWizard/SetupWizard.apk!/lib/armeabi-v7a, /vendor/lib, /system/lib]]
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at android.app.LoadedApk.makeApplication(LoadedApk.java:578)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at android.app.ActivityThread.handleBindApplication(ActivityThread.java:4680)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at android.app.ActivityThread.-wrap1(ActivityThread.java)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at android.app.ActivityThread$H.handleMessage(ActivityThread.java:1405)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at android.os.Handler.dispatchMessage(Handler.java:102)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at android.os.Looper.loop(Looper.java:148)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at android.app.ActivityThread.main(ActivityThread.java:5417)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at java.lang.reflect.Method.invoke(Native Method)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at com.android.internal.os.ZygoteInit$MethodAndArgsCaller.run(ZygoteInit.java:726)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at com.android.internal.os.ZygoteInit.main(ZygoteInit.java:616)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: Caused by: java.lang.ClassNotFoundException: Didn't find class "com.google.android.setupwizard.SetupWizardApplication" on path: DexPathList[[zip file "/system/priv-app/SetupWizard/SetupWizard.apk"],nativeLibraryDirectories=[/system/priv-app/SetupWizard/lib/arm, /system/priv-app/SetupWizard/SetupWizard.apk!/lib/armeabi-v7a, /vendor/lib, /system/lib]]
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at dalvik.system.BaseDexClassLoader.findClass(BaseDexClassLoader.java:56)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at java.lang.ClassLoader.loadClass(ClassLoader.java:511)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at java.lang.ClassLoader.loadClass(ClassLoader.java:469)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at android.app.Instrumentation.newApplication(Instrumentation.java:981)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at android.app.LoadedApk.makeApplication(LoadedApk.java:573)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: ... 9 more
10-08 15:36:55.273 2973 2973 E AndroidRuntime: Suppressed: java.io.IOException: No original dex files found for dex location /system/priv-app/SetupWizard/SetupWizard.apk
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at dalvik.system.DexFile.openDexFileNative(Native Method)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at dalvik.system.DexFile.openDexFile(DexFile.java:295)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at dalvik.system.DexFile.<init>(DexFile.java:80)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at dalvik.system.DexFile.<init>(DexFile.java:59)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at dalvik.system.DexPathList.loadDexFile(DexPathList.java:279)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at dalvik.system.DexPathList.makePathElements(DexPathList.java:248)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at dalvik.system.DexPathList.<init>(DexPathList.java:120)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at dalvik.system.BaseDexClassLoader.<init>(BaseDexClassLoader.java:48)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at dalvik.system.PathClassLoader.<init>(PathClassLoader.java:65)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at android.app.ApplicationLoaders.getClassLoader(ApplicationLoaders.java:58)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at android.app.LoadedApk.getClassLoader(LoadedApk.java:376)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at android.app.LoadedApk.makeApplication(LoadedApk.java:568)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: ... 9 more
10-08 15:36:55.273 2973 2973 E AndroidRuntime: Suppressed: java.lang.ClassNotFoundException: com.google.android.setupwizard.SetupWizardApplication
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at java.lang.Class.classForName(Native Method)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at java.lang.BootClassLoader.findClass(ClassLoader.java:781)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at java.lang.BootClassLoader.loadClass(ClassLoader.java:841)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: at java.lang.ClassLoader.loadClass(ClassLoader.java:504)
10-08 15:36:55.273 2973 2973 E AndroidRuntime: ... 12 more
10-08 15:36:55.273 2973 2973 E AndroidRuntime: Caused by: java.lang.NoClassDefFoundError: Class not found using the boot class loader; no stack trace available
10-08 15:36:55.275 740 931 W ActivityManager: Force finishing activity com.google.android.setupwizard/.SetupWizardActivity