Typical experiences of transgender people in academia?
(Original answer March 2015)

I guess it's time to answer my own question.  Not long after posting the original question I began living exclusively as a woman (barring some short family-related interruptions).

I'll list some themes that applied to me that I think would apply generally:


Work interruption: As much as I tried to avoid it, transitioning interrupted my work.  I spent a lot of time learning how to behave, e.g. to minimize the likelihood of being attacked, to know how to react when people ask intrusive questions, and so on.  Medically, you're sent to doctors, psychologists, psychiatrists, etc., who make you jump through all sorts of hoops over a long period of time.  The various surgeries trans people get can take you out of action for weeks to months.
Comments at university: There were some "hiccups" transitioning at university (smart people can make some really dumb comments).  However, they were a drop in the ocean compared to the hate I received from elsewhere.
University accounts: IT were totally unprepared for my transition.  E.g. my request for a Rebecca Stones email was refused and a subsequent email about the matter was ignored.  So my students referred to me by name X but email me under name Y which I found humiliating.
Bathrooms: There were a few surprised looks initially when sharing the ladies room with my female students and other female academics.  I never heard any complaints about it, and it didn't seem to be a big deal.
Applying for jobs: I have noticed no significant difference when applying for academic jobs in my area.
Academic record: It takes time to get your academic history records updated, which makes applying for jobs beforehand awkward.  During this time, I took up an adjunct position where administration requested a record of my PhD; I refused to supply this but indicated that several professors at the university witnessed me obtaining my PhD.  They refused to accept this, which resulted in a prolonged exchange of emails.  Eventually, I cited the university's privacy policy, after which they backed off.
Prior publications: I had to come to terms with having publications under my dead name.  I absolutely hate hearing or seeing that word refer to me.  I had to decide whether or not to include those publications on my CV and cite them in my publications (which could out me as transgender).  For my CV, I include these publications, but I list only the author surnames (I still feel uncomfortable with the thought that whoever reads my CV will Google these publications).  I cite them in my publications, as citing them doesn't directly imply that that name belongs to me.  I'm hoping I can bury these publications in new publications over time.
Travel: As an academic, I travel a lot.  Consequently, I have to keep in mind (a) attitudes towards transgender people when going through immigration (you're not at your most "passable" after a long flight), and (b) local attitudes towards and laws regarding transgender people.  E.g. I want to go to a conference in Chile later in the year, so I Googled "transgender Chile" and upon reading things like "had her face disfigured with a blowtorch" was a bit unsettled.

(Update August 2015)

I attended the conference in Chile (SIGIR 2015) and I'm pleased that my face was not disfigured by a blowtorch.  Here's a photo of the women's support group (I'm in there somewhere):



I'd also like to add:


Travelling can also interfere with (a) access to medicine, (b) access to [non-prejudiced] medical help, (c) other procedures, e.g. hair removal, and (d) the ability to buy clothes that fit.
Sometimes conference accommodation will be organized by gender (with or without the participants' prior knowledge).  This opens the possibility of being humiliated in front of colleagues (e.g. if the accommodation staff have their own opinion on your gender), and the possibility of sharing accommodation with someone who is uncomfortable with you.

Reacquainting with colleagues: I have a lot of international contacts, many of whom are still unaware of my transition.  From my experience, it's much better to meet in person than email someone an explanation (when all sorts of weird ideas about who I am can arise).  This is hard to do when your contacts are spread globally.
Transgender students: Transgender students seem to significantly appreciate that someone employed by the university is transgender.  Having a transgender member of staff goes against the stereotype that it's just undergraduate activists out to cause trouble who are transgender.
Online university resources: From my experience, university LGBT webpages cater almost exclusively to LGB students, with no usable information for transgender people.


(Update August 2015)


Male-dominated area: I'm currently in computer science which is kind of a "boy's club".  Outside of academia, being in a male-dominated career is sometimes used to discredit transgender women (among other things).  This results in a tug towards more female-friendly career paths, both outside of academia (e.g. nursing) and inside of academia (e.g. biology).
Female role models: It has become important to me to see and interact with successful female academics, especially those in my area.  (I was very encouraged by the healthy female presence at the SIGIR conference.)  Interestingly, it seems that I'm meant to be a female role model nowadays.
Female co-authors: I'm not sure if this is just a co-incidence, but I've recently found myself with a rapidly growing number of female co-authors.
International lifestyle: I'm currently a postdoc in China.  While I speak enough Chinese to "get by", and while my colleagues here are friendly, I feel isolated and lonely, and this is exacerbated by the lack of access to a transgender community.  (See also this question: Is feeling lonely and uncomfortable in my (foreign) country of study a valid reason to drop out of a PhD?)
Unwelcome attention towards my gender: Generally, I don't mind if people know that I'm transgender, as long as (a) this is not the only thing about me they consider and (b) they are not mean to me or my friends and colleagues as a result.  Thus far, to my knowledge, unwelcome attention has been negligible at university.  However, it's unclear if this trend will continue (after all, we only need a one-in-a-thousand to cause trouble).  Things I'm concerned about:


Maybe some transgender person somewhere does something evil, making headlines.  How would a university react to the resultant anti-transgender backlash?
What if a student makes a complaint because of my gender?  What if the student is well-prepared, having extensively read online anti-transgender literature?  What if the student makes a religious objection?
If I become successful and notable, hate material will probably be written directly about me.  Here are some examples (and it doesn't take much Googling to provide more examples):


  Boylan, a member of the all-male, all-white, all-heterosexual, all-middle-aged transgender leadership... (ref.)
  
  "Lynn" Conway, computer geek and head honcho of the raging autogynephiliacs who tried to destroy Michael Bailey. (ref.)
  
  Deirdre McCloskey isn’t a woman: wishing can’t make it so, not even wishing and flashing scalpels. Neither is Joan Roughgarden. (ref.)


Unwelcome attention from men: After meals, I like to go for a walk to get some exercise.  Consequently, I have now had three four unwelcome sexual encounters within walking distance from my office, during the day, and with other people around at the time.  I also had a male staff member in another faculty ask for "random sex".  I'm afraid to tell others about these incidents, fearing they might think I encouraged them (esp. if they attribute it to being transgender).  I also simply don't have time to waste sobbing about each one; they're much too frequent.

(In today's encounter, an elderly gentleman approached me and asked for the time.  I found my phone and gave him the time.  I also discovered his penis was hanging out of his pants.  He indicated towards some nearby bushes and said "gēn wǒ péngyou wáer", which translates to "play with my friend".  I walked straight back to the office, nearly in tears.  It's thirty minutes after the incident now, and I need to discuss a paper with a student.)
Paper cited during talk: Recently, one of my co-authors referenced our joint paper at a conference talk while I was in the audience.  I was not impressed that my dead name initials were on display, forcing me to sit there with that on the screen for all to see, and I was quite fearful that someone might ask if there was a connection between the two names.  If I had known that was going to happen, I would not have attended the talk.


(Update February 2017)


Surgery: I'm not sure if I should say this, but I ended up having "bottom surgery" back at the end of 2015.  It was the most physically painful experience of my life, by a long way, and the pain didn't go away until about two and a half months later.  So much pain.  During this time, my spoons were limited.  E.g. I'd go to the office to prove I still work there (I mostly just stared at the walls), and I'd need to spend the next day recovering.  I would bleed a lot, and this resulted in some additional accommodation expenses.  I would not be able to stand for longer than around 5 minutes without it being too painful (requiring a wheelchair at the airport).

I managed to go to the 2015 CMS meeting shortly after surgery, where Yuval Filmus (who I knew through math.SE) sat next to me just after surgery, although I don't know if he realized any of this.  (And I remember being a bit snippy with David Pike.)

The painkillers caused hallucinations, e.g. I'd be walking and suddenly "There's no floor! I'm falling!! Oh wait, there is a floor."  I became afraid of stairs.  This was happening while I was at work, although I tried to conceal it.  I also sent out a few "interesting" emails.

More than a year later, I have no regrets about having surgery.  It has resulted in me having a lot more confidence.  If someone denies my gender, they are simply being unreasonable (although, nobody ever does).  I'm now far less afraid that someone is going to find out about my past.
Bodily maintenance (dilation) is both time-consuming and painful, particularly at the start.  It's embarrassing but it nevertheless must be done, including while sharing accommodation with other women.  I got used to making "chit chat" while doing this.  Airport security sometimes inspect your dilators (which need to be in carry-on baggage) which can be embarrassing and worrisome (esp. when travelling through non-transgender-friendly countries).
Conversion to Islam: Perhaps contrary to popular expectations, Islam is a relatively transgender-friendly religion.  Often the attitude is that someone's gender is innate and decided by God, and being transgender is considered along the lines of a birth defect.  Of course, being Muslim results in its own complications (e.g. hijab).  I haven't had any problems praying in the female prayer areas (including on-campus ones).
A publication about transgenderism: Perhaps this is not a typical experience, but I published a paper about transgender bathrooms usage (here), which was mentioned in the Washington Post.