Hi Mike,
Found your thread and thought I might pass along a few thoughts to you. We did a huge CA trip in June/July '08...have a 4th grader who is studying our state history and wanted to show her and the whole family the sights. We had some great experiences I thought I would pass along. If they don't fit in this time around, maybe you can file them away for next time.
We did do one of the guided tours of Yosemite. In fact, we did the whole day 8 hour one with our kids, ages 9, 5, and 3. Now, we do have great little travelers and they hung in there just great, but at the end, my 5 year old turned to me and said, "That was impressive, but long."
(she is a little precocious) Anyhow, we were glad to take a tour to give us an overview of the sights, but in retrospect, we enjoyed getting on the shuttle and roaming, discovering those wonderful places around Yosemite Valley more than anything else. I saw someone else give you that advice and I so would go with that! We did enjoy some of the ranger activities, specifically the night star gazing for $5.00 a person. I am not sure if it is going while you are there, but you can look it up on the Yosemite website. THAT 2 hours was fabulous and my kids still talk about the constellations and stories the rangers shared. You do sign up for that and pay in advance through Delaware North.
In Monterey, not sure what your budget is, but we splurged (Pricelined the whole trip except for Monterey and Yosemite, so we thought, hey what the heck?!) and stayed at the brand new Intercontinental Clement Monterey which is literally right next to the aquarium. AWESOME location, but you'll need 2 rooms. Sometimes they have specials on their internet site when you pay in advance, so it might be worth checking into. Not sure how adventurous your kiddos are, but we have very brave and fun loving ones. While at the aquarium, our daughter took advantage of the kids' intro to scuba lesson which was AMAZING. They do a kids intro to surface scuba right in the part of the outside aquarium where it meets the ocean. No special skills or equipment needed. We did it spur of the moment and they outfit them with everything. VERY, VERY fun.
If you have the opportunity, another highlight of our trip was the night tour of Alcatraz in San Francisco. We read a great kids' book about Alcatraz history to the kids before we left. The night tour is SO neat; our girls LOVED the slight creepiness of it and the "Sounds of the Slammer" presentation they do on the night tour. The cable cars are a not-to-be-missed; we didn't do too much at Pier 39 or Ghirardelli Square, although I know there are tons of folks who swear by them.
Have fun! You will have a blast!
Jeanette
PS: BE PREPARED..... We consider ourselves a huuuuuuge Disney fanatic family, but in Yosemite, our 10-year-old said, "I love this place more than
Disneyland" and in San Francisco our 5-year-old said, "San Francisco is my new favorite place!" YIPES! Sounds like you might need those days in Disney to keep them on the straight and narrow, haha