Perhaps the first thing to stay away from is calling her "the little lady", else it will a honeymoon without the honey!
Sounds like you have it sorted ...
Kuta: close to the mall on the beachfront, you can take boats to Kuta reef for Airports lefts and rights. Lots of fun. If your wife's a beginner, you can do some social surfing with her on Kuta beach (which is kak, but has a great vibe).
Bingin's way cool for bodyboarding, and from there, if you want to explore, you can hire scooters from Nyoman & Nyoman close to the beach - Ulu's is close but you will get so-o-o lost, I swear. Also, on big days, there's Padang, between Bingin and Uluwatu.
Nusa Dua isn't the greatest place for surfing as far as I know, but again, you can explore from there. There are three waves on Nusa Lebongan, none of them too great, but who gives a crap, you're in paradise, right?
Go to
http://www.wannasurf.com/ and look up some of the places, they will give you lists of the local waves, and ratings. Very useful.
That's it - a useful tip I got from Billy Miller, is use Blue Bird taxis - they have meters, while the rest run on guesstimation!