While not guaranteed, I believe the risk of yellow fever is low. We did not experience any mosquitos in the area. I believe the Panamanians spray these areas to reduce any chance of malaria.

It would be much safer to book a trip with the cruise ship as there may not be any bus back and the taxi would be expensive. The trips that the various cruise ships do are good value generally. At the cruise terminal there are various tours that you can take but just watch the time as the cruise ship doesn't wait for non cruise booked trips.

The experience at each is quite different, best is to do both (I was there in March). Miraflores has a big visitors center, with excellent historical exhibits and 2 viewing levels. You can spend a lot of time there. It is also crowded. Aqua Clara is smaller with no exhibits, a short movie to watch, and not crowded. Watching the ships is good at both, a little better at Miraflores if you can get up to the fence.

Yes they do as it is huge business $$$$

HI, You do not have to book nothing in advance. Right after you leave the ship next to the pier you will see a big line of taxi/vans which will take you wherever you like including the a.m. The prices are fixed and they are well below the prices taken on board.

Llegando a la ciudad de Colon, esta el desvio para el centro de visitantes de Agua Clara, no necesitas entrar a la ciudad para ir a las esclusas. Yo fui en carro rentado, por lo tanto no sabría decirte si hay buses desde la estación de trenes.