Sugru's damned useful for adding this sort of thing. I swear by it.
Whilst I've only used it to fill a couple of cracks on my Pandora, on my 3DS I used it to extend the rubber feet on the inside of the lid (the ones on the first units are a millimetre or so too short, thus allowing the surround of the lower screen to leave marks on the upper one - Sugru quite easily put an end to that ).