Good on ya. Keep in mind that unless you're feeding yourself absolute garbage, your body is going to decide what to do with what you put into it, and there's no magic food that will make you gain/lose weight or muscle. There are a decent number of people who can be elite athletes and literally eat snickers bars and french fries. There are also people who have metabolisms that just require that they really limit their caloric intake to be athletes. It sounds like you are in the eat-anything camp, basically, so if gaining muscle mass is your goal, you are basically just going to have to consume more calories than you burn, do a lot of low-rep-to-failure type exercise, and make sure you get some halfway decent amount of protein. You may very well not gain any weight/muscle, though, because ultimately your body is going to decide on it's own what to do with those nutrients.
I should also mention that your goals are really not ones that dovetail well with adding muscle mass. Beep (for all practical purposes VO2max) test and 2 mile runs are both events that you'll do worse at with more mass, not better. Probably moreso the 2 mile than the beep test but really if you're looking for endurance, why are you trying to add muscle? If anything you should be going the other way. I can think of some sports (rugby, soccer?) where you need both some size/mass (at least in some cases, Lionel Messi being the huge exception) and some endurance (again, Messi, who runs less than anyone somehow) but in general if you're not a big dude, putting on a bunch of muscle is going to really hinder your ability to do well at the stuff you've mentioned.
-W