1) I am not sure if there is an additional meaning, but I would assume that any metal on the bag or inside the bag is hitting / rubbing against another piece of metal. The sound produced would be known as the onomatopoeic word 'clinking' (to clink).
2) 'To be thrown/to be thrown off' means to be surprised by an unexpected event. It has a negative connotation in American English, and is more of an unpleasant surprise, than a happy one. Feelings of dismay and disappointment may also be attached.
3) 'To tap away' means to press one's finger against something. In this case, she is pressing her phone's screen. You can also tap away at a keyboard. It is not 'tape', but 'tap'.
4) 'to be scuffed' means that the object's surface is hidden from view by marks made from something else. If I scuff (verb form) my shoe, I can no longer see the white part of my shoe, and now it is covered in a dark mark.
5) I am not sure what 'nail passages' are, but the sentence in question sounds like it could be referring to NASAL passages, which is just one's nose. If your nasal passages are assaulted by something, you really do not like the smell, and you cannot escape from it.