It could be his molars, but honestly I doubt it. Molars coming in is something that would continuously bother him throughout the day, not just at 3am.
I would try eliminating/shortening his afternoon nap. 11pm is waaayyy too late of a bedtime for an almost 2 year old. Around 2 years we moved my son from 2 naps to one nap a day. It will take a few weeks to make the adjustment, but it was so worth it. My son is now 3.5 and we have eliminated naps all together. Whenever he takes a midday nap now for any period of time, he goes to bed late and usually gets up in the middle of the night crying. Once we eliminated his midday nap, he went to bed at his normal time (730PM) and stopped getting up in the middle of night. Of course we still have the occasional nightmare wake up about once a week, but before that he was getting up 3-4 times a week.
You might also want to flip through a couple of baby sleep books. My favorite is "Healthy Sleep Habits, Healthy Child". Another one that I hear a lot about is called the Baby Whisperer. None of these books will have the "Magic Cure" but take what advice you can use from them and do what you think is best for your son.
We also now have a 15 month old daughter and I still re-read "Healthy Sleep Habits" to refresh myself on what my baby is going through at each stage of the game and what my 3 yo is going through as well.
Good Luck!