I now have an extra folder on my external HD that is greyed out which I think is the migrated library -
Aperture Library 3...plibrary.
What is the full name of "Aperture Library 3...plibrary."?
After you migrated the Aperture Library to Photos you should now have two libraries:
- The original Aperture Library: It should be named like before, but with the filename extension ".migratedaplibrary", for example: "Aperture Library.migratedaplibrary". The icon will still be the Aperture icon
- The new Photos Library: It should be named like before, but with the filename extension ".photoslibrary", for example: "Aperture Library.photoslibrary". The icon should be showing a fan of three pictures with the rainbow coloured flower.
Are you seeing these two libraries on your external volume?

If the filename extension of your Aperture Library has not been changed from .aplibrary to .migratedaplibrary, Photos has converted a different library or the conversion has not been successful.
If the file chooser dialog is showing you the original Aperture Library as greyed out, it is perhaps still in use because the migration is not completed or it is damaged in some way, or your external volume is not compatible with Photos. Can you enable the "Ignore Ownership on this volume" flag as described her?
Move your Photos library to save space on your Mac – Apple Support
And has the external volume been prepared as stated by Apple? The correct file system format? And locally mounted, not accessed over the network? If you cannot enable Ignore Ownership, there is something wrong with the volume.