David, Ben Johnson had a fantastic squat and deadlift, of course he was on winstrol but he still had to train.
Squat heavy, build strength up. As that strength increases you need to work the fast twitch fibers to make yourself powerful and explosive. Power Cleans will help with the explosive part of it.
Perform Better has a speed and agility section that has some good stuff in it.
For now do what Steven suggests. Most 100m runs are won in the first 50m. Not many HS athletes have that 5th gear to turn it up like we sometimes see the elites one do. Its all in how fast you are off the blocks and how quickly you accelerate and maintain top speed. Work that hard.
Get stronger and do some drills to increase explosiveness and quickness.
I also suggest medicine ball work - http://www.medicineballs.com/education/howto/howto.html
especially the drills where you are bouncing the ball of the thighs explosively as you stride.
And to answer your question about training the entire body, yes. Have you ever seen Ben Johnson, Usain Bolt, Carl Lewis, etc.? They are not "smooth". They are muscular. Sprinting hard means your arms are pumping hard, your core is working and your entire body is working together to keep you running fast.