OK, so I actually got it working!
This is how I did it:
I took UbisoftGameLauncher.exe
UbisoftGameLauncher64.exe
ubiorbitapi_r2.dll
uborbitapi_r264.dll
overlay.dll
overlay64.dll
from C:\Program Files (X86)\Ubisoft\Ubisoft Game Launcher.
I then pasted them into [GAME DIRECTORY]\Assassin's Creed 2\UL
(UL folder being from the mod). This causes the new version of UPlay to run with the mod, meaning it can communicate with the servers. I now have may Uplay items in AC2 this way
.This makes the game read from it's actual save-file folder, not the mod's save folder - while still preserving the Black Bar fixes. So your actual save file would be in
C:\Program Files (X86)\Ubisoft\Ubisoft Game Launcher\savegames\[Unique Profile ID]\4.
If you want to use saves you've already started with the Black Bar Fix mod, all you have to do is disable cloud saves for AC2 in Uplay, and then copy the saves from [GAME DIRECTORY]\Assassin's Creed 2\UL\Storage\Skidrow\4 and paste them into C:\Program Files (X86)\Ubisoft\Ubisoft Game Launcher\savegames\[Unique Profile ID]\4
then launch the game as you would normally, and you'll be up and running! This should also mean you can use older save files with the Black Bars fix too.