Hi Lori,
Definitely talk to your LBS about what wasn't comfortable during your maiden voyage on your new bike!
It's possible that some or all of the discomfort is related to the "new position" (compared to your old bike) -- even a subtle change (such as saddle height up or down by half a centimeter) can cause some discomfort (legs, back, pressure on arms/hands) at first, and that is why making gradual changes in bike fit is critical.
It's also possible that describing the pain/discomfort to the shop where you bought your bike will set off some 'red flags' regarding fit isues, and the shop may be able to swap out components (to change things like stem length/angle, handlebar width and height, seat position (fore/aft, angle, height)) or tweak your fit a little more to make you more comfy.
Don't be shy ... the LBS is there to help you. They want you to be happy with your bike and passionate about cycling for a long time. Plus, you'll save a lot of your own time by asking them for help!
Monica



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