Out of 'his' league?

A couple of months ago I was asked by the new head of IT to help ‘test’ a few systems he was setting up in our office. I work as a designer and our programs are very complex and require a great deal of IT attention. We spent a few weeks testing some new features and improving old ones. I was supposed to help Mike one day test a new feature, but was unable due to an emergency client meeting. I sent him an email on my way out, saying I could help later in the week. While in my meeting I received a response from him and at the bottom read: “how was your meeting”. I was a bit surprised, but took it as a nice gesture and responded. A few one line emails over the next few weeks evolved into daily multi-paragraph emails, long talks and finally lunch. All that of which I greatly enjoy.
I will be the first to admit, that Mike is not the typical guy I am attracted too. He is far from the typical tall, dark, and handsome. But he’s amazingly intelligent, funny and he can always make me smile. He has never ‘hit on me’ and is always very professional. I find it cute that he is so nervous around me and he rambles when he’s nervous and I’m pretty sure he didn’t actually eat anything when we went to lunch! He is also the poster of “IT guy”. The other designers in my department think he’s a ‘dork’ and seldom communicate with him, as they hate his long winded tech explanations as to how he solved the latest computer hiccup. He’s off beat, he’s a total IT geek (as he calls himself this), he likes Lord of the Rings and other movies I have never heard of. He plays music and writes sci-fi fiction stories. All things, that in the past, would have made me turn my snobby nose and not think twice about. Oddly I’m attracted to his intelligence and I’m intrigued by his talents. Our talks have evolved and last week, we finally both ‘admitted’ we have started to have feelings for each other. I have had a share of scumbag men, who are more interested in how much they lifted at the gym and how fast their motorcycles are than how my day was. And those relationships usually get to a point that they only respond if I send them half naked pictures or there is ‘sexting’ involved. It is nice to FINALLY talk to someone more interested in me than my age or how I look.
Last Friday night, we talked and I told him I was really falling for him and I was enjoying getting to know him. After our conversation, he sent me an email with the subject: “why me???”. In the email, he basically told me, that he just wanted to know, why him. “of all the men you could have, and in my estimation you could have any man you want, I'm simply curious… why me?”. I was a little taken back by this email. I KNOW he is not overly confident in himself and you can tell he’s never been the popular guy in the ‘in’ group. He seems to have this belief that I'm ‘perfect’; young (as he is a few years older than me), beautiful, intelligent, and on and on. All in which is very flattering, but how can I make this ‘geek IT guy’ see that the ‘hot girl’ of his dreams is really into him and how can I encourage him to be confident enough to go for it?