Brandon,
Welcome to the site and feel free to look around at other people's stories for inspiration. I don't think I've ever come across a gay man who was already in a long term relationship with another man that thought he was a transwoman before though. Not to say it hasn't happened, I've only been around here a month now.
Have you heard of the term genderfluid? Basically it means that you don't choose to identify as any single gender all the time. Your gender identity changes from month to month, week to week, day to day or even hour to hour! There's nothing that says you have to identify as one gender or the other, you could also choose to not identify with either gender! So, you could go to work in boy mode, and party all night in girl mode!

Does something like that sound more like what you're brain is telling you maybe?
Also, Just as there's gender fluidity, there's also sexual fluidity, and the two are not linked. I say this because there's no guarantee that just because you want to be a woman (sometimes or all the time), that your partner will leave you. Some transwomen keep their penis if that's the concern for instance. You don't HAVE to have gender reassignment surgery just because you're trans. There are many instances of heterosexual couples surviving the transition of their spouse to become basically a homosexual couple, so there's no reason why it can't work the other way too. If your partner loves you as a person, and presuming you don't radically change who you are at the core of your being, then there's nothing saying he can't continue to love YOU, not matter how you present yourself to the world around you.
So in conclusion:
1. Hang in there, keep the lines of communication open with your partner.
2. Find a therapist or someone else to talk to about this who's not biased.
3. Explore your gender identity in a safe environment. Nail polish is a great start, but now go buy some pantyhose, panties, a skirt, or something else and see how you feel around the house.

Mascara is a great start too.
4. You are who you are on the inside. Don't deny your inner feelings, they'll only get stronger with time and denying them can drive you to do irrational things once the pressure builds up too high.