I am running a Spigot server version 1.12.2. Pex works fine until I put my old custom ranks and permissions in to the permissions file. When I do that, pex stops working completely

I recommend copy the old custom ranks file called it "permission Copy" and then delete the "Permissions.yml"
then create a rank again with permissions.

Unfortunately PermissionsEx is currently unmaintained and no further updates are planned. Because of this, all issues are being closed. If you are looking for an actively maintained permissions plugin, take a look at LuckPerms. It is compatible with major server platforms and can import data from PEX.