This question I can actually answer, since I am the one who has a long, hard history with USCIS that is full of drama

The short answer is: no, you can not apply as a male. Because technically, you are applying based on a residence of 5 years on a green card and you are marked "F" on your green card. If you apply as a male they will simply not accept your papers and return them to you along with the uncashed check.
You'll have to change your Naturalization certificate later, when you do all the changes on ID and social security.
Or you can do all the changes on ID, social security etc and apply for replacement green card with M mark on it and later apply for citizenship as a male.
However you can change your name in Naturalization process to anything you please, you don't need a doctors note for that, even when changing from female to male name, but not the gender.