Second on the stretching...should do daily. Back strain can be referred into leg pain, but a more upright position can help with that, as does having a strong core. The more upright position can also take some stress of your hands, shoulders and neck. This is why touring bikes have a more upright position because a long time bent over, craning your neck to see can get very old quckly. My knees rarely hurt, but I keep my saddle high enough so my heel barely touches the pedal on the downstroke. I've found this makes it easier to spin and works your calves more which works the quads a bit less. The less pain you have the less tired you will be.