Is it possible to use drush migrate-import to import custom fields?
I am currently working on a similar migration and had a similar problem. In my case the custom fields were part of the Profile2 module in D7. I installed the D8 Profile module and added a patch that fixes the Profile2 import

https://www.drupal.org/files/issues/2018-05-16/profile-migrate-from-profile2-D8-2957256-4.patch

After that, the custom fields were automatically created, populated and linked to the correct user.

Not sure if that is what you need.