Hello LostSoul,
I can imagine your dreams, your hopes, your plans... are in a bit of an upheaval at this point. How will the future that you envisioned mesh with the future that now could be?
Sometimes it really helps just to take one day at a time when there is an amount of confusion and uncertainty. I also recommend therapy for both of you, if at all possible. If that is not possible, at least you have open communication going for you at present. As long as you have open communication, honest communication, in your relationship - anything is possible.
If I allow the blind optimist in myself to reply, I would say that in the end it is the same person you met and fell in love with together. It is at the core, the same person that loves you even if the package and presentation changes.
I'm usually not that hopeful though, so I won't say that.

In fact, if I was really out of my element, I would say that love takes an ordinary relationship and allows it to not only continue but thrive through extraordinary circumstances, when both partners are committed to making it work.
But I don't feel out of my element today, so I'll take another approach and just relate to you as best I can.
I am TS (MtF), bisexual and am in a relationship of 7 & 1/2 years. A relationship which started as me presenting male 24/7 and not even acknowledging myself that I was trans.
Fast forward a few years, my boyfriend had grown to know and love the male person I presented myself as.
But after some deep emotional turmoil within myself, brought on by several deaths in the family, depression, repressed feelings, and more... I had to admit the fact that something in my life was completely wrong. And I knew if I wanted to keep my relationship with my boyfriend, I had to talk. And I had to be honest.
It was extremely difficult and very emotionally taxing at first. I had spent years of learning how to be the strong, silent, unresponsive and confident male I unfailing presented myself as. Hehe, that all went to crap. I didn't even know who I was for a few months. It was scary.
I have to give credit where credit is due though - my boyfriend was very supportive and at the very first thought of my being transgender, he said he supported me no matter what and would love me no matter what - he just wanted me to be happy.
I was afraid he wouldn't be able to love me anymore. I was afraid I couldn't be his partner because I truly wasn't the male I thought he dreamed of. But through months and months of talking, sharing and exploring together - we found that he wasn't looking for a 'male'. He was looking for 'me'. And he wasn't going to give up unless that is what I truly wanted.
And to this day he loves me more than ever, and I him. I'm a lot more open than I used to be. So many walls have been broken down. I am a lot happier and healthier. And that has actually benefited our relationship in a few positive ways I believe. Especially as of late, it's been quite exciting to grow closer and more intimately than we ever have.
Sure there are some minor quirks for us at present, but we've gone from being two lost people to a couple who is secure enough to laugh with and embrace each other through what used to be awkward, embarrassing or unsure moments.
Anyway, I'll stop rambling. Maybe this won't help at all. I just wanted to chime in and say that if you truly do not feel like throwing in the towel at this point, then don't. It may be the best thing you can do for both of you.
I wish you the best in your relationship.