Mark,
I just did the same thing myself. It looks like when I copied over a user with my custom role assigned to them, I got a copy of the role in v1.9.1. Try restoring a course with a user that is assigned to customrole. You will still need to reassign the users to the System Role, but, it looks like the role was copied over correctly.
In the end, however, I created a new role. I needed to dig into the new permissions for 1.9 anyway. The attached spreadsheet (in OpenOffice .ods format) is what I used to help me document the process. Turns out I only needed to make about 5 changes to have the functionality I was looking for, as opposed to the 35 that I made in 1.8.
Roles and permissions
Migrate Custom Roles
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