Whats the right object identifier(s) to use internally in internal filing systems so that the migration to DOI names can be reasonably painless?
A DOI name can incorporate any existing identifier as its suffix, so you can adopt anything you like. But that’s only part of the question to ask. In any consistent information management scheme, you have to also answer the question of what precisely is being identified. To do that you have to assign some metadata. If the metadata is not consistent, then you will have problems later. Use of DOI names will enforce a consistent approach to identification and metadata and is another benefit of using DOI names even for material which is not public.
