One of the reason that I post questions like these is to get this information out where it can be seen. I figure if I have the questions, others likely will too. I could/can get many answers from calling people direct, but that wouldn't get the information where others can see it.
Besides, I enjoy this forum.
With that said I have done some due-dilligence of my own reguarding the above. According to the Water Taxi service, pets can ride up to the point of the officials calling for "Evacuation". Not any real 'new' news there. They also said that they prefer pets crated unless they are under control and not causing problems. Finally, the quietes departer times from SP to Belize City were listed as the 8am or 9:30am trips.
I'm sure it's also posted elsewhere, but here is the link to the water taxi: http://www.cayecaulkerwatertaxi.com/
Still questions to be answered in the original post, but it's a start.