1.) What I did was submit the application as female, and then on my own afterwards I called the department of resident life at the university I was going to attend. Resident Life professionals are very, VERY sympathetic to the LGBT population. I work for resident life at my university, and at least 75% of the staff actually is lgbt, and that's common at almost every university. let them know the situation and let them know your parents can't find out. they'll be respectful of that and work within those giudelines to get you where you need to be.
2.) I didn't do this--instead, I worked with the resident life department and the office of LGBT affairs at my university to get my name officially changed before I matriculated. however, if that's not an option, just go for blunt so it sticks in their head. either "hey, my records say sally but I go by steve." or "hey, my records say sally but I'm trans, so I go by steve."
3.) google the health center at your university, call or email them, and ask if they offer it and if so how would you get it.
best of luck!