How do I add a custom field to a Fusion filter if it doesn't come up in the list of fields to choose from?

Just copy an existing one to notepad and exchange the DE: part to the custom field you want, then copy it back.

In order to get to a field in Fusion, it has to be "tracked" in Workfront. Just add the field to your update feed here: https://YOURDOMAIN.my.workfront.com/setup/update-feeds and it will show up in Fusion.