Tuff,
Thats sounds a bit better.I would have a protein shake 'between' breakfast and lunch and one right after the gym.Don't substitute shakes for balanced meals.If the fat and calories are low in your diet then you will obviously burn more off than you consume don't EVER skip meals!
I came across a very good website last night with a fat burn calculator,take a look and work out your ideal target heart rate:
Target Heart Rate Calculator Tool – HealthAtoZ.com
Keep up the running if you are comfortable but don't over work that knee.It might be advisable to spend a couple of weight training sessions a week,building up the muscles around both knees with some leg extensions.The vast mojority of footballers i know aim for a physique that involves a lean,light upper body and big,thick,musclular legs.This keeps stress on the knee ligaments at a low.