I know this isn't the answer you wanted, but that's normal.  A bike fit will help, but if you think about how your body is positioned for the aero position, you'll realize that it's going to take some getting used to.  One of the big reasons I was excited to get a trainer this year was so that when Spring rolled around I wouldn't hurt so much from re-acclimating to the position.  You'll build muscles like with anything else and get used to it.  From what I've heard about that course, you won't spend a ton of time aero, though... lots of hills!  Good luck!