I don't think you need to "transcend" the itching or pain. It's about accepting the itching and (moderate) pain. If it's "clinical" pain (i.e. really bad), then by all means attend to it!
Itches, as @fivebells said, can be a really good teacher during meditation. They have all sorts of sensations and mental formations that come with them... great for insight.
A benefit of yoga and meditation practices that I think is overlooked is the development of patience. People tend to fall into a pattern of geting in a hurry about wanting to be more flexible, more mindful, etc then becoming more accepting of the progress they have and appreciating the practice for what it is. And then later becoming impatient about their progress... etc. But I think over time - at least for myself - the stage of accepting your condition as it is becomes more steadfast and the tendency to become impatient wanes.
I do three prostrations before and three after a meditation session (three = buddha, dharma, sangha). I find it really helps set the tone for the sit, as well as eases the mind into/out of meditation.