To make moves easier, I am putting together a major upgrade for release in 2.7.0 later today. It will save all necessary files to the .zdn file and ignore unnecessary files. That should make saving and loading .zdn files a bit cleaner and also help with portability.
As for now, just move the SysnativeBSODApps directory that you had on your previous system into your user profile directory, i.e. C:\Users\John
The _jcgriff2_ folder is deprecated and no longer used by the apps.
For the .chm file issue, don't forget to check the .chm properties to make sure the help files are unblocked. Unblock Files in Windows 8 using PowerShell and Registry - Michael Crump
