Usually uncomfortable hands are a sign of handlebars that are too low. The lower your handle bars the more weight you shift forward on your hands & arms and smaller & less supportive the seat you require (since there's less weight on it). The higher your handle-bars the more upright your body position and more weight you shift to your seat, and hence you need a bigger seat else your butt will go sore & numb. Maybe you have a long torso, that shifts weight to your hands/arms. I find comfort & speed do not mix, the most comfortable is upright sitting and the fastest forward and low... somewhere there's a balance for you.

I can't really answer why you have a sore arm, I can't say I've ever had sore arms from biking my hands are another story when I'm riding a bike with a straight bar or a road bike where I'm low and a lot of my weight is forward on my hands my hands kill.