Really cool story. How did you deal with the safety issues in Afghanistan and Pakistan? Were they a real concern, or is that mostly overblown by the media?
You should not group Afghanistan and Pakistan together. Afghanistan is not a safe place to visit. Pakistan is absolutely safe as long as you don't visit the western tribal region. Land in Lahore, travel to Islamabad and then to Peshawar and northern areas. You will have a good time. Lots of tour companies also arrange the trips. If you're feeling more adventurous, you can visit Multan, Bahawalpur, and Karachi.