First - you are using arms and shoulder muscles in new ways, so some soreness is not unusual. Nervousness and anxiety may be causing you to tense up, and maintain a death grip on the handlebars. Relaxing your hands, arms, and shoulders will help a lot.
It looks like the reach might be a little long. And the bike looks awfully short in the photo. Your seat could probably be raised quite a bit, and that will change how your arms and shoulders fit the handlebars.
Most people ride with hands on the hoods, with only occasional forays down to the drops. 2nd-3td fingers restong bit not gripping, the brake levers, but think along the lines of "shaking hands with the hoods." That should give you the correct position. You don't need to keep fingers on the brakes all the time, but be able to slide into position when slowing, or if a stop is anticipated. It will become second nature eventually.
And finally, you may need to slide the seat forward a little provided it still keeps your "knee over pedal" position reasonably close.
But, first you need to get the seat position - height, and fore/aft locked in. Then address the reach and handlebar issues. You may need a shorter stem on the handlebars. Your shop where you bought the bike should swap out the stem at no charge if you need a change.
If you try to work out handlebar adjustments before the seat height - well you'll just have to do it all over again when you raise the seat. I don't think you are doing yourself any favors by keeping the seat so low You will get used to a higher seat, and in the long run a more comfortable position, a lot faster than you think, especially when all your parts aren't hurting any more.



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