It seems to me that the best sex involves lots and lots and lots of talking about what everyone involved wants and needs, and plenty of creative visualization by all partners, in order to get past the "wrong junk" issue.
My BF was a good little Catholic virgin from a conservative town when we started dating, so I had to have some extremely awkward conversations about anatomy, how conception worked, how birth control worked, and so forth. It was mortifying at the time, but I'm glad we both got on the same page early on. Being able to talk about your body, even if it makes you uncomfortable, will save you a lot of discomfort and resentment in the future.
Even with all the clear communication in the world, though, FtM anatomy can be threatening and foreign if you've never interacted with it before. It feels different, smells different, and reacts differently to stimulation than cisgendered male or female anatomy. It can also be very intimidating to someone who feels confident in his ability to please cisgendered partners, but totally lost at sea when it comes to pleasing FtMs. It's like being an awkward virgin all over again, rather than an experienced sex partner. And in addition, the FtM partner may be extremely uncomfortable with sex and intimacy, and may be turned off by seemingly innocuous words or touches. It's tricky. It's walking on eggshells at first.
It may take some time for your boyfriend to come to terms with all this. I'd definitely give it time--getting over any negative or anxious feelings he may have could be the beginning of something new and amazing. If, in the end, it doesn't work out...just remember that's okay. Sometimes things don't work out. You learn from them, you enjoy them while they last, and then you move on to something even better. I found it was much easier to enjoy intimacy with my partner once I let go of the fears I had about his ability to be attracted to me. YMMV, of course, but it really reduced my anxiety. I realized that the worst that could happen was that we'd stop having sex. We'd still be good friends, so I knew I'd never lose him completely.
If you'd like to talk about anything sex and intimacy-related in specific, feel free to ask here or by PM. I;m not an expert or anything, but I;m happy to talk if that would help.