bowow: Now THIS is an area where I have to give the Pro's their props! That is the concept of "Exercise Prioritization". (Do I sound like a Weider Ghost Writer? Oh well...)
Anyway...if you have a lagging body part, it simply takes priority in your training. So...1) You hit it FIRST 2) You hit it HARD and 3) You hit it OFTEN (within reason and if not impairing growth). Also, since your lagging body part is legs, you may have to eat bigger. (Be careful, because it sounds like you may have a tendency to put on fat). (P.S. No...the running did not mess up your legs. They were probably more fat than muscle to begin with...and keep in mind that increases in STRENGTH are NOT synonymous with increases in size). Hope this helps!