Thanks for the details, Michael. Do you have a dev environment on IIS that you can test the latest version (2.1.4.8) with?
I'm wondering how good the wp-mobile-detector plugin's multisite support is. Normal process would be to create a new site, and individually activate each plugin for that site, correct? (Or do you have that mobile plugin activated network wide?)
The Cloner process is to clone everything directly and bypass all that. Normally this works fine. But if there's non-standard dependency that the mobile plugin relies on the activation process every time for something then that will inherently not be compatible with the Cloner. Based on the FAQ that states:
I am getting an error that it was unable to install correctly. What do I do?
Please try deactivating and reactivating the plugin.
...and looking at your log where it isn't finding that plugin's config file, I'm wondering if that plugin #1 requires activation every time and #2 stores its settings in a flat file rather than the options database table where it should.
If my assumptions are correct it will not be compatible with the Cloner. However, it is quite likely that the following scenario could still work for you:
1) Build a template site without the mobile plugin activated
2) Clone the site
3) Activate the mobile plugin on the new site
It's an extra step, but could still save you a bunch of other configuration steps outside that mobile plugin.
The Cloner log write is completely expected behavior. If that main file doesn't exist at first then it gets created so that it can log clone operations.
Hope that helps. Thanks!