I prefer to use the term 'Process by Lot' if you are using the GUI
Calibre has a CLI and a number of folk do OS level 'Batch Processing'
For the stuff with
Good metadata. Process by big lots is probably OK
'Good' is a vague term

Series info is NOT a DC standard and is missing from a lot of books

.
You might want to do those each 'by lot'
BTW
Manage Series PI can be a great help tool in assigning order (best with a contiguous series group)
Search the Internet PI to help resove all sorts of metadata issues that the Basic 'Get Metadata' can't resolve.
'Patience Grasshopper'
Nibble away at your backlog (those not in the Library). Clean a bit as you go rather than face 5K of OMG, I still need to fix this