If I remember correctly, the checksum and whitelist files should be generated on the fly on the first launch.
1. Try removing
ULMServerLinkBook.inf, and
ULMLinkBook.inf if you have that too (those files determine which books are displayed in the bottom row in Relto).
2. In Uru Setup (
Uru.exe), in the Connection pane, try checking “Update all ages on launch”.
Now, just to be sure:
3. When you wrote you downloaded and installed the patch from the GOG page, you meant the
full installer of
Uru: Complete Chronicles, right?
It’s usually better to use a new install, somewhere else than “C:\Program Files”.
4. The DI patcher you used is the one from
this post? That's the only official patcher.
5. You didn’t use Drizzle? It shouldn’t be used to install fan ages with Deep Island, the shard has its own downloader.
6. You mentioned you have the Ferry Terminal in the Nexus. That location is in the “City Locations” panel; check that you have a “Restoration Links” panel. If you don’t have it, or it’s empty, something didn’t work.