We have been fortunate to have special instructors come in and let us practice the invasive pelvic exam stuff on them as they taught us. I only did the male one so far, but I was amazed at how much we could push and prod without hurting the individual (the level of sensitivity of course varies person by person). But, it helped me get over that fear of hurting the patient a bit, cause the instructor literally told me it wasn't hurting as I was doing the exam, and encouraging me to be less afraid.
Basically, I think it takes more to discomfort the patient than we think (still, early on, it's probably best to err on the side of caution). Anyhow, just keep at it! You're definitely not the only one that's nervous with these exams. Doing my first breast/pelvic exam on a female next week, and I'm nervous too. Just trust that you'll get more comfortable and better over time.
Heck, I even get slightly anxious when I have to check the point of maximal impulse on a female patient. I think it's just a matter of, the more you do, the better you get at it.