Take a close look at the saddle angle - is it tilted slightly downward? If so, adjust it until it is nice & level; that may help if you are having lower back pain. When I bought my bike the saddle was angled just a few degrees down and my lower back was just killing me - the guy leveled it out, and I've not had a back problem since.

If you're feeling too "stretched out" you may also want to have some other adjustments made to effectively shorten the length of the cockpit and give you a more upright riding position. This could be along the lines of either using a shorter stem, or rotating the bars up, or changing the angle of the stem to raise the bars, or sliding the saddle slightly forward (note on saddle sliding - that may also take your knee position out of whack so don't do it if your saddle is already adjusted correctly). As you ride more and start to ride more aggressively, you may eventually want to return to a lower riding position.

I'm not really sure about the legs aching, where does it hurt & what type of pain is it?