It looks like the new bike has the saddle higher than the old bike, a longer reach from saddle to bar, and bar about the same height as the saddle instead of higher than the saddle. You might want to check that with a measuring tape.
Not being able to see you on either bike, we can't say which bike fits you or if either does. The old bike looks like it was set up for a smaller person than the new bike, and for a slower, more upright riding position.
A significant change in fit can certainly cause strain and pain if you go right out and do a long ride in the new position. Even if the new fit is actually the better one in the long run. It is possible to get "used to" a bad fit. You need to give yourself time to adjust. I would not go changing bar or stem or bike right away. Give yourself a couple weeks of shorter rides. While you are adjusting, pay attention to exactly what is straining or uncomfortable, aching shoulders tell a different story than sore knees for example.
There are some very basic fit guidelines that you can check. When you are on the saddle with pedal at the lowest position, your knee should be bent a little, somewhere around 25-30 degrees. When you pedaling, your hips should stay pretty stable, without rocking a lot right and left. When your hands are on the bars, and you then briefly lift your hands off the grips, you should be able to hold your torso in the original position without straining hard. When the crank is horizontal and pointing forward, the front of your knee should be generally somewhere over the pedal, though doesn't need to be exactly over the pedal spindle.
The bikes are different, which may be affecting you. The old bike is a "comfort bike" meant for a rider who sits heavy in the saddle, relying on the suspension to absorb bumps, and rides slowly, in an upright and inefficient position. The new bike is a little more of a performance bike, the rider uses her anticipation and her legs to absorb bumps and is expected to be riding faster, in a more sporty manner. You can probably tell which bike I prefer, which makes no difference to which bike you should prefer . . . But the point is, you will have to do a little bit of adjusting when going from one bike to the other.
I phoned the bike store yesterday and explained how i was feeling and the person I talked to said the bike was a poor fit for me. They said no matter how much we tweak anything it will never be a good fit because of my height and it being a guys bike. They said i could exchange it for something more fitting in a women's bike. 1st choice was an Alight 3 which I didn't care for bc it had the step thru frame. Then they showed me the Alight 2 had the top bar. That one cost a tad bit more but I liked it. I took it out for a test ride and felt so much better on that bike the handlebars were so much closer. The guy took some measurements and tweaked the saddle and handlebars into an even more fitting position. I am very happy with the purchase of the Alight 2 =) I plan on taking it easy on the bike and kind of pace myself so I can adapt it being it is way different than my old comfort bike. Thx all =)