I am so happy to see a new cruiser and one going to Mexico.
I really urge you NOT to let paranoia get the best of you. A few things you may or may not know.
English will be widely understood almost every place you go. By the same token there is no need to take money for souvenirs because you can get local currency from any ATM if/when you need it.
Most shops will take credit cards (even your bank debit/credit card) and in a nice shop I would not hesitate to use a credit card. For one thing, you still get consumer protection if for some reason your purchase goes bad (fake gold, or something).
I would rather see you taking ship offered shore excursions rather than see you walking around alone in shopping areas -especially in Puerto Vallarta. Just because that one tour was robbed do not think it had anything to do with it being a ship-offered tour.
The fact the banditos targeted a ship tour shows how brazen and frankly stupid they were - but I would still be far more wary of being on my own or with a "local guide" you do not know.
Yes, I realize most local guides are very reputable - but ship tours are still safer in the long run - especially if something bad happens you will have a local contact - but please do not worry about that unlikely event.
I think you will be perfectly safe. Surely the best and safest shopping will be in Cabo - plan to do most of your shopping there.
In Puerto Vallarta you can enjoy the beach very close to the ship, and they are all Hotel-controlled, so no banditos there. You can swim, parasail, eat at the hotels, etc. The water is warmer in PV than Cabo or especially Ensenada. A wet suit will still help, though. I have been swimming without in both PV and Cabo, but a wetsuit will make it more tolerable.
Mexico is not a great place for snorkeling (like the Caribbean) but is a good place for the beach, with real waves (not ripples like you get in the Caribbean). Once again, banana boats, parasailing, water-skiing are offered on the beach in PV.
Cabo is great for shopping and GOLF (if you do that) with many competition-style courses. Horseback riding is another option.
Ensenada is a typical Mexican town - seedy, cheap souvenirs, tangy Mexican food and cheap beer. Enjoy it for what it is and be sure to see "Hussongs Cantina" a well-known local bar.
I have not been to Manzanillo in many years - sorry no advice.
Keep in mind the ship will be a big part of your vacation - not just the ports of call. Enjoy the ship and consider spending some money on special food and drink onboard rather than tours. You will enjoy the ship just as much as the destinations - probably more.