Well we are certainly no SF experts we have only been there once. We stayed at the Westin St. Francis, it was very lovely. Our favorite thing in SF was Alcatraz. It was really pretty cool and overall one of our top things from all our vacations. Taking a trolly car was pretty neat as well. We actually walked the Golden Gate Bridge and then walked back. Sounds a little crazy I know, it took about 45-50 minutes but everytime we see it on TV are like "we walked across that". Fisherman's Wharf was okay, but we didn't think anything too great. Ghiradelli was fun. The shopping was also great. We only spent about 3 days there as we did a road trip from DLR to San Fransciso on the Pacfic Coast Highway. We stopped in 3 places on the way up.
DLR is great fun and the VGC are amazing! Staying there is a real treat to say the least! The DLR portion of this board will be able to help with planning for both DLR and I am sure you can find some San Fransico advice as well.
Enjoy the trip sounds absolutely amazing and I am sure you will have an awesome time!