Melusine, it sounds like your Shadowkeeper install didn't go according to plan because SK isn't indexing your BG2 resources. If you have the zip/exe file you may want to reinstall it and create a folder for it. You may need to configure it to point to your BG2 folder (it should normally find this on its own).
With custom items, especially ones with TBG and IAP extensions you need a program like
Infinity Engine Editor Pro to import the TBG files into your override. If it's just an ITM file you can copy directly into your override but it won't have any text. Sounds like you did the right thing.
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Memnoch - Custodian of the Holy Flame 