The other things that gets nasty are pensions, lawsuits (see Littleton v. Prange in Texas where a wrongful death lawsuit was dismissed because the dead person was married to a post-op transsexual, so the court decided that the spouse - a post-op transsexual - wasn't really female and thus not really married, causing the wrongful death lawsuit to be dismissed), insurance claims, end of life decisions, and hospitalizations.
To the original poster:
I'm not a lawyer, so my opinions may be worthless.
I'm in a very similar situation as I am married to someone who was misclassified as male at birth. The two differences are that we don't have any legal ties to Massachusetts or Florida, and my wife is not pre-op. Each state is different, and each state can do what it wants thanks to DOMA.
The ID card is only part of your problem. I do not know of any state that doesn't allow same sex marriage AND would consider the marriage of a cis-male to a MTF in transition to be legal, sadly. Of course it's fairly untested water in most places still, but, sadly, Florida has *really* bad case law right now. In 2004, Florida courts decided that a FTM post-op person was legally a woman in Florida's eyes (this was a divorce case - he married a cis-woman, and the woman was able to get the marriage declared invalid). Unfortunately this means that someone who hasn't transitioned would definitely be considered whatever sex is on their birth certificate for marriage purposes. Because the State views it as a same sex marriage, I suspect the Feds would too if you lived there. It's the state of Anita Bryant, sadly, so it's a particularly hard place to be. Sadly, the same also likely goes for Pennsylvania, although I'm not aware of any case law there for marriage (it's conceivable a Pennsylvania court could actually do the right thing, but I wouldn't count on it).
For the case in Florida, see: Michael J Kantaras v Linda Kantaras.
Ironically, in some jurisdictions, my wife would be considered male and could only marry a woman while in others she would be considered female and could only marry a man. It's a huge, huge, huge mess. We really need to take gender out of marriage, and we really need to get DOMA repealed.
You might be able to be considered to be married by people in either state, but I'd be very, very cautious. Don't make the wrong person mad (it's likely criminal, not just civil, if you represent yourself as married on anything legally binding like taxes and such), and the person suggesting criminal investigation doesn't need a direct tie to you. You also may be denied access to your spouse at the hospital and in other situations, so make sure you get good legal advice. So do be careful. That said, there's a lot of people like you out there - we just live in the shadows hoping that nobody has reason to challenge our love. It's really sad that a country founded on the principles of religious freedom would seek to impose religious views on people, but that's a whole other rant.
As for the ID card, I'd suggest you (or her) call the Florida DMV and ask about the specifics (don't give names if you are worried about that) - make sure you mention if she had an ID card there in the past and such that the gender marker has been legally changed in another state and she wants to move back to Florida. It'll probably take a few transfers to get a good answer. I'm *guessing* that she'll have no trouble getting the ID card with the right gender on it, but I'd verify it. Note however that the ID card, regardless of marker, won't make your marriage valid there, sadly.
I pray for the day when love, not bigotry, dictates what is a legal marriage.