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is the nandroid just a standard thing, or is it something i need to install?
As I remember we need to have USB debugging enabled for SuperUser Permissions to work. We can see this answer directly came from Paul in Modaco forums.
Yup, i can confirm that. Ran modaco for a few weeks before i got around to repartitioning my SD card, once i'd done that it did all the apps2sd setup automatically.I've heard that it deals with it even if you've already been using it and installed loads of apps.