If your marriage was legal before, it will be legal after transition.
The federal government considers the marriage contract to be permanently set at the time it was signed, meaning that if the genders were non-matching at that time, subsequent transition does not invalidate the marriage*. (However, this is federal policy and not yet enshrined in law. It's always possible for them to pass a law which changes things.) The couple may end up fighting with various bureaucracies who don't realize this, but it IS a valid marriage.
My guess is that in it would be hideously complicated in a state that doesn't recognize same-sex marriage, yes. Presumably federal policy and inertia would work in one's favor, but it probably would be a problem every time a bigot or a hopelessly confused bureaucrat got involved. I cannot imagine that Florida law could override federal law, but it's theoretically possible so long as it's only a federal "opinion"; if I were you, I'd research the laws carefully AND I would demand that any bureaucrat who objected be able to cite chapter and verse on the law they claimed invalidated your marriage. It may even be worth calling in an actual lawyer (or a cheaper paralegal!) for an hour or two of doing that research, so that you can have it readily to hand to present to naysayers.
*
http://www.opm.gov/diversity/transgender/guidance.asp"If the employees in transition are validly married at the time of the transition, the transition does not affect the validity of that marriage, and spousal coverage should be extended or continued even though the employee in transition has a new name and gender."
