I know other people have disparaged leg extensions and leg curls, but after I injured my knees (many years ago, coincidentally when I was in the Navy), I started doing leg extensions, first with light weights and up to a hundred reps and gradually with heavier weigths and lower reps (although I still stick with 12-15 reps) and the heavier the weights got the less knee pain I had. Now I run and squat a couple times a week and occasionally have a little pain the next day in one of my knees (the one I finally had to have surgery on). My recommendation is do whatever you can to strengthen the muscles around the knee (leg extensions and squats), and running will only get easier in the long term.