1. Yep, the default one is always named "default". So the tag for that one can be <j> instead of <j=default> as a shorthand. When re-importing, uncheck "default" to keep your updates to it.
2. Ok oops, that one folder is actually different from the rest, since it just contains the default materials STM uses when a new object is created, not anything related to the tags iirc. What I meant to say was: when *re* importing, leave the resources folder unchecked, so the data in there doesn't override your changes that were made. You can also specifically uncheck different subfolders.
3. Getting a fix is all that matters! Glad you have something that works!