OK, the .wdmc folders are hidden in each of the other folders which contain data files (pictures, movies etc) and are where the device keeps the thumbnails, transcoding information and other items that it needs for web access. Personally I find the things a complete nuisance and a very poor way of holding such information rather than a centralised database, but that’s another story entirely.
Anyway what I would do in your case is to put both your MyCloud and your MyCloud Mirror onto your network, and then open each in a separate Windows Explorer window on your PC (I’m assuming you’re using Windows - if you’re on a Mac or Linux box then do the equivalent). Then make a new folder on your MCM (call it “transfer” or something) and then drag and drop the root-level folder(s) from the MyCloud into that transfer folder on the MCM.
Doing that should then cause the whole file/folder tree from the MyCloud to be copied as a fresh transfer into the MCM. For 350GB it may take a while to achieve, but leave it running and it should get there eventually. You can then do some housekeeping and put the files/folders exactly where you want them, but only once the transfer is completed (don’t try it whilst it is still in progress).
It may also be worth to set Windows Explorer to show hidden files/folders (on my Win7 machine it’s under the view tab in the tools > folder options menu item, maybe somewhere a bit different if you’re on a different version or OS). Then you should be able to see any hidden files/folders such as the .wdmc folders, and it will give you a better idea of what is actually being copied.