Jan,
I've spent a lot of time in Indonesia over the last 10 years ('92, '94, '96, '98), including about a month on a part of my honeymoon in '98. Each trip took me through Bali.
To be helpful to you, it might be helpful to know a bit more about you and how you like to travel. Where are you staying on Nusa Dua? What kind of budget are you working off of?
Here are some thoughts.
Ubud - Great, enchanting little town that is getting bigger and more touristed, but still incredibly charming. A visit to Bali wouldn't be complete without a few days visit. It is very relaxing and has great food, shopping and nearby attractions. Consider staying at Ibah (expensive) or Pita Maha (super expensive). Both have website. There are some fabulous restaurants in Ubud. Don't miss the famous Cafe Wayan and the Dirty Duck.
The chain of Aman Resorts originates in Bali. They have some of the most amazing accommodations you will find anywhere. Check them out at
www.amanresorts.com
Consider scuba diving around Cemaluk (Amed) along the east coast of Bali. (I've had better luck here than on the north coast at Mengangan.)
Lovina - This beach town was getting rundown when I was there in '98. Most of the resorts are a bit run down and hurting for business. I would definitely spend time in Ubud over Lovina.
Lombok - I don't know if 2-3 days is really enough to visit Lombok, given you have to either take a ferry or fly there, each taking up at least half of your day. To get to the Gili islands (a bit redundant as Gili means island)you would need to take another boat from Lombok off the north coast. The Gili islands have fairly modest accommodations. There is some nice beach and snorkeling, but the crowd is decidedly young and there isn't much otherwise to see if you are looking for "sights". I love Gili Trawangan, but I also don't mind staying in a bamboo hut with a squat toilet and a mandi out back.
The rafting trip is good fun. I would highly recommend it.
To help you understand my suggestions, I'm currently in my mid-30's, live just down the road from you in Sacramento, and have traveled by backpack extensively throughout Southeast Asia and Europe. I utilize the Lonely Planet guides and the Moon Publication "Handbook" series as my primary sources of information for Southeast Asia.
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Happy Travels,
Rhinochaser