Gender stopped being confusing for me when I stopped thinking about it and just went with my feelings.
Often that's easier said than done, though. There's one little word that the conscious mind loves to throw around. When you think you have your feelings nailed, are more than happy to go with them, when it all seems so clear... one little word which throws a spanner into the works and makes everything suddenly seem as clear as a muddy lake.
"Why?"
Three letters that make everything infinitely harder than it needs to be. Three letters which make you suddenly question everything you feel, everything your instincts and intuition insists to be the case.
I've found that many times, people know what they want, and who they are, from a place deep inside themselves. Call it Psyche, Higher Self, Soul... no doubt you can think of other terms. But that one little word comes along to force one to explain it. To attempt to rationalise, to categorise, to justify.
"Why?"
Why am I like this? Why do I feel this way and not the other? Why do other people's views cloud my own? Why is everything so intangible? Why can't I be happy? Why should I believe the way I feel? Why can't someone just tell me who I am?
That one little word. It confuses the surface of our mind. The part which has to have an answer for everything. It attempts to force us to explain a state of being. It attempts to force us to grab on to the nebulous mist of instinct and emotion with both hands, and place it under an analytical microscope. It attempts to draw on parallels to rationalise. Masculine, feminine, traits, hobbies, dress sense, observations... "Why?" Creates checklists. Formulas. Benchmarks. Tests one must pass. Quantification. Qualification.
All to satisfy a relatively small part of oneself. Like a rower attempting to alter the flow of a river just through paddling hard enough.
For me, things stopped being confusing when the answer to "Why?" became "Why not?"