I know this topic is several months old, but I have info that will help as far as a Florida drivers license is concerned. You can get the gender marker on that changed with simply a letter from your endo/hormone prescribing doctor that says you have completed or are in the process of a gender transition. You want the wording to be precise on this letter just in case your DMV representative decides to be a hard ass about the rules.
The FL DMV follows the same rules as the US State Department, so you can follow the letter guidelines here:
http://travel.state.gov/passport/get/first/first_5100.htmlI know this works because I am pre-op, but I changed the gender marker on my license when I changed my name (May 2012). As for the birth certificate, I don't know about the gender marker, but as far as the name change, you just need to mail a copy of your name change judgement, pay a fee, and fill out a former. The downside is that they put a notice on the bottom of the birth certificate that it was amended. Literally: on X date, name was changed from MALE NAME to FEMALE NAME. I don't know if they will do the same for gender, but I think that's completely screwed up. Your birth certificate basically outs you to anyone who sees it.
A ray of hope though: I read another thread on here a year or two ago where someone changed their name and gender on a Florida birth certificate, and it had no mention of the amendment. Maybe it was because she went through a law firm, and they specifically requested that not be added.