You'd probably have to ask them specific questions, and I'd do it in writing to make sure, but it does say on the web site:
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The Amtrak Explore America fare permits travel between the same two cities once in each direction.
There are some exceptions: You may travel up to twice in each direction between the following cities only:
New York City - Albany, NY
New York City - Washington, DC
Washington, DC - Charlottesville, VA
Chicago - Joliet, IL
Chicago - Battle Creek, MI
Salt Lake City - Grand Junction, CO
Browning, MT - West Glacier, MT
Los Angeles - Barstow, CA
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On the other hand, unless you are expecting to take more than 30 days to do it, I would think it'd make more sense to pay a little more and get the North American Rail Pass which makes the stopovers unlimited as I understand it, and:
(from the web site)
* Your trip must include at least one journey between the United States and Canada.
* Your trip must include travel on Amtrak and Via Rail Canada.
* The last trip taken with the pass must end before midnight on the last day the pass is valid.
* Pass holders must obtain a ticket for each trip.
* The pass may be used for a maximum of four one-way trips on any given leg.
* Other restrictions may apply.
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Which lets you have a max of FOUR one-ways on any given leg.
So the N.A. RaillPass gives you more flexibility.
The way I read the Explore America pass details, the number of stopovers is NOT per region, but total, per purchase, so if you bought separate one-region passes to get more stopovers (that should work) you are now spending what a N.A.Railpass would cost anyway. Of course, if your (separetely purchased) regions happened to intersect at a desired stopover city, you would be in luck, since that would not be considered a stopover, if you have separate region passes (at least as I interpret it).
If you purchased a separate Florida Region Pass, and either begin or end your travel in Florida, you could begin or end at MIA, stopover at ORL, and TPA or JAX, then end (or begin) the Florida Region Explore at either PNS or SAV for a few days (not counted as a stopover), and begin the rest of your Explore travel there on the next region's fare. At least that's how I read it. Purchasing Florida separately would give you three more stopovers elsewhere. But the North American Pass still strikes me as a better deal (and more flexible) if you want more stopovers.