When you say you’ve got stuff all over the place I’m guessing you your expansion kits as well as your libraries? Are they all on the same drive and is that drive just for samples? I.e NOT your C-drive?
You will have to ask for new licences for BFD1 and BFD2 libraries. They are now respectively Eldorado and London Sessions.
If you’re running your old BFD1 and BFD2 libraries in BFD3 along with all the presets you, ‘shouldn’t’ get duplicates.
I would recommend having all your libraries on one drive or at least all the audio data from those libraries (preferably an SSD).
I have mine set up on an SSD with a master folder called BFD Drums, inside that folder are my other libraries in their own folders so I have BFD3 Core library, 8 Bit Kit, BFD Delux Kit, BFD Jazz Noir, and so on.
I’d say it won’t make a lot of difference whether you set them up like that now, or after you’ve migrated but you’ll have to rescan your folders if you do it afterwards.
Also there is an updated version released this week which should address some of the earlier migration issues. Here are the release notes
Hopefully your experience will benefit from the bug fixes.
Hope that helps
Steve