Kaboom is a great choice. KFOG has the live concerts going most of the day and then the fireworks show is typically awesome. I don't know if this is true, but someone told me that as this is one is relatively early in the year, potential clients of the fireworks company come to see what they'll be offering this year so the company pulls out all the stops. They do things I've never seen other places - such as send fireworks up that explode and then leave behind flares that slowly fall to the water as they're attached to little parachutes. The ballpark is right there and there's a game on the same day this year, so it will be crowded down there (definitely use public transit).
I've been through Oakdale a lot, but never been to the festival. It will give you a look at a very different part of California - the rural, small town part.
There are no trains similar to the Napa train in Sonoma. Sonoma is great and home to some wonderful wineries though, so do spend time there. I went on the Napa Wine Train years ago and enjoyed it. It's the kind of thing you do once. I thought they did a nice job restoring the cars. There are many great restaurants in the area with far better food, but you're paying for a different experience with this.
Check with the rental car company, but I generally find they like it when cars are being dropped off at the airport and often don't charge extra (once in a while I'll rent a car from near my home to take to the airport to avoid parking because that can work out cheaper). The other way around doesn't work as well because you have all those airport taxes.
Have fun