Hi Ken,
Thanks for the thorough report!
It's interesting to know that I actually did very similar trip from August 12 to 16 also with Jim Silver of Aqua Adventures. I led a group of 10 divers from Houston.
On Saturday, August 13, we went to MUSA & Machones reef. The visibility was still crappy due to the remnant of Hurricane Earl than went to Belize.
On Sunday, August 14, our original plan was to swim with the whaleshark, but I was told by Jim that there won't be any whaleshark tour so we switch our cenote diving from Monday, August 15 to Sunday, August 14. Like you said it rained all day & made the entry to the Little Brother became quite interesting. We had to follow & trust Rafa direction to blindly get down into the mud hole until the water cleared up about 10' deeper. We almost lost one diver at the end where she followed a line below her instead of the one next to her. Rafa ended up went back into the mud hole to chase her down.
On Monday, August 15, we tried to go again for the 2nd time for the whaleshark tour, but the harbor master closed the port again due to the same problem, so we ended up just hanging around town. It was just a bad luck for us. We heard also the whaleshark tour on Tuesday, August 16, the day when some of us were going home, the whaleshark tour was also cancelled.
Two of my dive buddies were smarter than the rest of us to stay longer till Saturday, August 20 & had a chance to swim with the whalesharks on Wednesday, August 17. They may have dove with your group on Thursday or Friday that week.
I'm still patiently waiting for the refund from Jim on the cancelled whaleshark tour. He must be busy with running his shop at this peak whaleshark tour season.