Incident 1:
I have two office mates  C and A (names are removed) that know me pre-transistion. One day they asked me about the process of transitioning and I talked about it. Then this guy S walks in the office. He knew me before. S then asks me questions that are invasive (basically do you have a dick/were you born with male parts). I evaded the questions by not really answering them, but S assumed I had female parts. By the way that conversation went he came off as a person that would say you need to find the right man.

Incident 2:
C, A, S and I went out to eat at the school food cafeteria for dinner. S asked questions the have you fingered yourself and have you had sex with a man. I was uncomfortable, but I don't think he or the others noticed.

Incident 3:
We all were in the department lab and S said that he wanted to ->-bleeped-<- me. S said that C and A wanted to as well. Nothing happened but I was massively uncomfortable. S and C make my alarms go off.

Since A, C, and S are friends I don't know if anything would hold. The only other person in the lab was wearing headphones. Also I'm not sure if it counts as sexual harassment due to the school policy.

Sexual harassment:
unwelcome sexual advances, requests for sexual favors, and other verbal or physical conduct of a sexual nature when or such conduct has the purpose or effect of unreasonably interfering with an individual's work or school performance, or creating an intimidating, hostile, or offensive working or studying environment.

If I report it S could get suspended or other noticeable things. I'm in a small department and even though there is a non-retaliation part of the rules I would feel uncomfortable with a lot of people knowing because certain punishments like suspension would be noticeable.

IMO, you were sexually harassed. No woman would put up with being asked "Have you ...ed yourself" or "have you had sex with a man." I can't imagine a social situation where those questions would be appropriate, and certainly not in a place of work. The fact that you're not female doesn't change your right to propriety.

Agreed, this is sexual harassment and should not be tolerated by you or your place of work/school (was hard to tell from the post which). You have the same rights as everyone else to retain your privacy about your person and your experiences, and 'S' crossed so many lines undetected (by C and A) that it's unbelievable and flat-out disgusting. You don't have to tolerate this kind of harassment/abuse, ever.

REPORT at once. Disgusting perverts.

Yep, sexual harassment. Honestly, some guys. If you still consider the friends - tell them you will not discuss your gender or sexuality with them at all from this point on. If they do then report them. If you no longer consider them friends reports them. Seriously this kind of behaviour confounds me.

Ohhhh yes, most definitely sexual harassment. Do a clearer write up of everything that's happened so far and keep a notepad around to jot down anything that happens from now on. Get it all together and take it to your supervisor or HR (depending on your company's policies).