i had a wonderful time at the duathlon training this morning, and i used a TT bike for the training.
i recently acquired this bike and only had few miles before today, and i had a difficult time getting comfortable in the aero position. controlling the bike is not the issue, the problem for me is my shoulders got tight and sore right away when trying to ride in the low position and also have your head up at the same time. i ended up riding 90% in the upright position and my time was very similar to my road bike.
i think i just need to get accustomed to this new position.
Have you thought about getting fit for you new bike? The fit for a bike with aero bars is very different from the normal road bike.
if you didn't get a professional fit for the bike get it.
even after you get a professional fit there is still an "adjustment period" for the fit as the aeroposition is not the most comfortable position to be in.
but then again opinions on tri bike fit and how it should look/feel/etc can be even more diverse than any hot button political issue you can think of.
Agree that you need a pro-fit on your new ride but your body will take some time to adjust to the new more aggressive positioning and you'll likely feel it in your neck and shoulders. However, if you ride consistently, it shouldn't take more than a few rides...that's been my experience.
I had the same issue last year when I added bars to my road bike, not only my neck and shoulders bothered me but lower back too. It took a few rides to get used to but it's fine now.
Also, I realized my bars were a little too short so I went to Cycle Life down in Georgetown and they took video and realized I needed a new stem which extended my position out more, that helped too. Getting fitted somewhere or at having someone look at how you're riding can help.