1) After the click that you hear when you open up the system, it should take a small bit of effort to get the top screen to wobble.  Although I cannot know the extent of your wobbling, the top screen is supposed to wobble when in any position other than the position that you get when you hear the click.  If it wobbles no matter what position, then you will need a repair.

2) The design of the 3DS, and all the previous DS systems, makes it so that the bottom screen and top screen never actually come into contact with one another.  Furthermore, both screens are flat and do not have anything on them that could scratch the other screen.  It sounds like a foreign object scratched the screen, which can often happen.  A repair is needed to correct this.  Also, I doubt that Nintendo would replace the screen itself; they would most likely just replace the whole 3DS.

3) The warranty is limited, in that heavy physical damage to the system could void the warranty.  It is completely up to Nintendo's discretion whether to fix the broken R button or not.

4) No matter what you send in the 3DS for, Nintendo will always transfer your downloaded games, downloaded videos, and ambassador status to the repaired 3DS.

It sounds like you should get a repair.  To schedule a repair, and ask them more about the R button, please call Nintendo at 1800-255-3700 (6am-7pm, Pacific Time, 7 days a week).