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Question 1: There are only charter flights between Miami and Santiago. However, Aerogaviota and Bahamasair fly directly from Nassau to Havana. As for Miami-Havana flights, American, Delta and Frontier airlines are launching regular nonstop services now in December
Question 2: Sure, if the CBP asks you about the reason for the amount of entries, just explain it to them. I don't see why it should be an issue - you're not overstaying in the WHTI area after all, nor are you violating the Terms of the VWP.
Nowadays when using APC kiosks, they reportedly ask you far fewer questions in most cases anyway.