Definitely check how everything is dialed in. Make sure your LBS folks see your positioning on the bike and agree that it makes sense (though don't let this work completely against your own ideal comfort). Perhaps the length from seatpost to bars needs to be checked? I do recommend the bar-ends. I've gone back to flat bars on my Racers recently, and though I love how simple they are, I really did miss the added hand positions that bullhorns/drops once offered me. I finished covering some bar-ends yesterday to add to one of the Racers; I'm sure it will help for rides longer than 20 minutes (my position-change threshold).

One other thing to question is the width of the flat bars...do your arms have to converge from a parallel position in order to meet the handlebar grips? Or do they splay away from one another to reach the grips? Opinions on this will vary, but for me, I find that keeping my arms parallel is key to a comfortable ride, shoulder- and neck-wise.