Sounds like you covered the ports! In Cabo, you can take a private operator boat ride out to the Arches. Cheaper than the ship's tours. But disembark as early as possible for that one. Also recommend sampling the food. Great Mexican food all around you! And bring your binoculars and be out on deck whenever possible when at sea as there are dolphins and whales to be spotted everywhere! Enjoy.
I'm going on that same cruise. Just under 11 days .
The one tour that I would never have anyone I know go on in Puerto Vallarta is the tequila factory tour. Did it a few years back. All it is is a tour of a building with old replicas of what they used to use to make it. Very boring. The one good part was the free samples they gave. A co-worker went there this summer and said he went on it and had the same fellings.
Be carefull in Cabo if you take a private tour. The ship leaves at 2pm. That doesn't give you a lot of time to do much. If you are on a cruise line tour, the boat will at least wait for you if you are late.
P.S. I checked the weather yesterday and there is a tropical depression off P.V. Should be gone by the time we get there thankfully. Although, it is always fun to have one night of rough sea's to add a little change to the nightly routine.
Celebrity Mercury - Hawaii
Princess Golden - Meaxican Riviera Oct/Nov '07
Norwegian Star - Mexican Riviera Oct '06
Carnival Ecstasy - Catalina/Mexico April '02
Disney Wonder - 3 day Bahamas Nov '99