Not sure what would interest you...also, I went to all these places before I had my Viper, so I don't know how Viper friendly they are. With that said, here is a list of things that I like in the San Diego area ( not neccessarily in this order):
The San Diego Rail Road Museum. It is about 45 miles east of SD
Pacific Southwest Railway Museum
The San Diego Wild Animal Park. They have the best bird show I have ever seen. I believe this used to be the Lion Country Safari where you drive your own car through the park of free roaming animals. I remember having Ostriches trying to get in the car when I was a kid.
San Diego Zoo's Wild Animal Park
Then there is the Main Zoo.
San Diego Zoo
SeaWorld
San Diego Park Home
And one of my favorite places, Balboa Park.
Balboa Park
They have a decent Air and Space Museum,
San Diego Air & Space Museum - Balboa Park
a small Automobile Museum
San Diego Automotive Museum - Balboa Park
and a rather nice Scale Railroad Museum.
San Diego Model Railroad Museum - Balboa Park
These are just a few of the things to do in Balboa Park.
Old town is nice as well the Sea Port Village for outdoor shopping along the water front.
Old Town San Diego Guide
Seaport Village - San Diego
As far as Hotels I will let one of the locals make the suggestions. My Grandmother lives in La Mesa, so we stay with her when we are down there.
I hope this is some help to you.
I am sure that you will have a great time! San Diego is a great place!