My best advice - keep working on core strength and hamstring flexibility (hip as well). This will open up doors for you in the fit dept. It'll take a while...
Second tip - when the bike shop sets up your bike...if it has 4-5cm of spacers under the stem...you're either on the wrong bike or not flexible enough. Search for bikes with taller head tubes.
Lastly, clip-ons are not evil so don't think you'll automatically pick up 3mph from an ill-fitting tri bike.

http://www.slowtwitch.com/...de_Bike_Fit_649.html

Dan put everything all in one place. Read all that page and all the links and you will understand bike fit better and be better off than most triathletes.

Other than that, I'll make just one comment. If you are using a road bike with clip-ons and are using the regular length aerobars, then it is very likely your hip angle is very contracted. For a lot of folks a road bike is probably best, but you have to shorten the reach so you are not too extended.

Otherwise, read the above link and learn.

Chad

The very first response to this thread was a strong one- advising you to do some fitness work to improve your ability to sit on the bike with a stable core for an extended duration.

Fit and position are an important part of the equation, one that can't be overlooked. You have to start with a good fit and then have a workable position built onto that fit as a start point for optimal comfort.

Along with that, specific training to address any weak points such as sore shoulders and neck, sore lower back and habitual saddle discomfort will help you acclimate to sitting on the bike more effectively. You have to work to meet the position half way.

To some riders, a fitting is shortening the reach, raising the bars and putting on a gel saddle. Then they are "comfortable". There isn't anything wrong with that approach. If the goal is greater balance of performance and functional tolerability then the fit may require more work.

Go to a good fitter, do work to address your own weak points such as frequent saddle discomfort or lower back/upper neck soreness and build a relationship if possible with your fitter to continue to evolve your position as you evolve as an athlete.

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Tom Demerly
The Tri Shop.com