There are some things that you just have to do for yourself. Having been in a similar situation, I went to the administration, told them that I was going through transition and needed to opt out of gym. At the time, I was starting at a community college and gym was required.
You need to have your name legally changed and as soon as you can, have your gender legally changed. Go through an attorney to make sure that everything is legal and correct. Once you do that, you can have your social security changed, your driver's license and every other paper work changed. It sounds like a major pain in the butt, but it saves a tremendous amount of explaining and having to get around the system just so you will be treated by your preferred gender.
My Driver's license was the easiest. Once I had the name change and social security, I just walked into the DMV, told them that the gender on the license was an error and could they please change it. No questions were asked.
I think you will find life easier if you get these changes. What the requirement for being legally male or female can vary from state to state, so you will need to find out what your state requires. Any official changes that require paperwork are things you need to save, forever. If you need to use them, you will need the originals and just copies won't be accepted.
I'm glad you are returning to school. Getting a degree is more important now than ever. The job market is very competitive and a degree gives you an edge.
sam1234