Once you get some miles in, you'll know soon enough what you want to change, if anything. The more you ride, the more you're going to want a harder, less-padded saddle. You may end up changing the stem so that the handlebars are lower. But maybe you'll do neither of these things.

One way to make bike commuting easier is to do it half the time, at least as a trial. Put the bike in the car on Monday morning and drive in. Then ride home. Then ride in on Tuesday morning and drive home.

You may want to show your riding position to someone at your local bike shop if you're looking for recommendations on getting more comfortable on the bike. You may learn that your seat is too high or low or forward or back. Or something like that. I worked as a mechanic in a shop last year, and most inexperienced riders had their saddles in bad positions.