Its hard to troubleshoot this without seeing a pic of you on your bike. But, I can tell you that I am 5'4" and ride a 44cm bike if that makes you feel better about the size. I have to sell you though, that depending on the manufacturer, I can straddle bikes ranging from 44-51 cm. I bought the 44 to get the seat tube angle and top tube lenght I required. If your bars are 1 cm narrower than you shoulders, that could be your problem. I would recommend going 0-2 cm wider. I went from a 37cm to 40 cm to 41cm bar, and much prefer the 41s (my shoulders are 40cm). But, your saddle fore-aft should be set up to get your knee over the pedals, not to bring you closer to the bars. Stem length and height should be adjusted to modify reach. You can get neck pain when the reach is too long, too short, bars too short or long, or from being too stiff on the bike and not shifting position enough. Its best to have an experienced person look at you as you are riding to troubleshoot, or post a pic for us to look at of you pedaling in a trainer if you have one.