I've had a tremendous amount of hand pain with my new(ish) bike, so I'll share what I learned from trying any number of things. Hand pain can be a function of a number of variables: the bars and how they are positions, the hoods and how they are positioned, stem length and rise, and saddle position both height and fore/aft position.
I'd start with getting your saddle positioned correctly. Not only will that maximize your power on the bike, it will hopefully get your weight properly balanced over the bike. You ideally want the majority of your weight in the rear of the bike, such that you are not bearing too much of your weight in the your upper body. Not only is this more comfortable, it also makes your bike handle better.
I would echo the advice that you raise your saddle to where your shop originally placed it. Ideally, you want the greatest amount of extension that your hamstring and knee can handle.
As far as fore/aft. Most fitters will tell you that knee-over-pedal-spindle is just a rough guide. I'm a bit farther back on my saddle than KOPS--by a couple of centimeters if memory serves. There's a limit with my current set up of how much more setback I can get. I'm as far back the saddle rails as I can go and, if memory serves, I already have a seatpost with a fair amount of set back.
Getting your stem length and rise, along with bar position, is in my experience more trial and error than anything. At wits' end last year with my new bike. I went to a fitter that is an expert in biomechanics. We went through a process during the fitting where he had me pedal with my hands behind my back and then, while still pedaling, I was instructed to reach for my bars. He watched as I did so and more or less eyeballed where my hands were gravitating to. From there, he would reposition the bars and adjustable stem and start again.
Sadly, that expert fitting didn't relieve my hand pain. Because the original fork I choose for my bike turned out to be overly stiff, we just recently changed it. I noticed a big difference in my hand pain over smooth roads versus bumpy bad roads. I really haven't been able to figure out if it's going to help. We're otherwise at a bit of a loss. This was a custom bike. 
So, Catrin, all I can say is that it often takes a while to dial things in. I will say that with my first bike, I had a fitting at Nebo Ridge, and Jonathan got me set up extremely well. I hit the ground running thanks to him. I will second the advice to work some pilates or yoga into your routine in order to build core strength, too.
Live with intention. Walk to the edge. Listen hard. Practice wellness. Play with abandon. Laugh. Choose with no regret. Continue to learn. Appreciate your friends. Do what you love. Live as if this is all there is.
--Mary Anne Radmacher