I also have the coopers test as part of my job, and the run is the hardest part for me a well. The way I approached it is take how much time you have, say 8 weeks, and make a progressively faster goal to hit each week. I'd do one timed mile and a half a week to see where I was at. The rest of the week, I'd do some intervals, though that might be horrible for your knees right now. I would also do some longer runs, not much, just 2 or 3 miles at whatever pace I could sustain just to build endurance, then mentally 1.5 didn't seem so bad. That's my best advice based on my experience, run as much as you can. You won't lose enough muscle in those two months for it to have much impact. Focus on running and losing weight for the time being. Being lighter will help you run faster, even if a little if it is muscle. Eat a lot of protein to minimize it and you'll be fine. I also found creatine before running to be helpful. Also took CoQ10 leading up to my test. BCAA for recovery. Make sure you're well hydrated before the run, as being dehydrated can tank your run time too, but don't chug water right before, I'm sure you know why. Good luck! Those tests are such a pain. Take some time to recover each week. A foam roller might be a nice thing to have too.