That's a good plan and something a lot of people don't do, they'd rather sit in front of the TV.
I personally have to make it more structured than that for me to be motivated to do it... otherwise other life stuff gets in the way.
Don't think I can run a mile with my knees but I'm in the shape to do it, and can do all the rest of that stuff with ease. I could probably bench 215 18-20 times if I just laid down and did it... never really tried to see how many pull ups I can do, but I've been doing 4 sets of pull downs, then 3 sets of 10 pullups after that... so... Just trying to get back into squats, kills my shoulders to hold the bar on, but I'm working on it.
When you squat, is the bar on your back? If so, try doing lighter weight and front squats instead. You'll get a very good core workout and it'll put less stress on your back/shoulders.
My lifting routine is fairly simple and pretty old school. My days consist of Back/Biceps then Chest/Tris then Legs/Shoulders. After 6 weeks I rotate to Back/Chest then Bi/Tri/Shoulders then Heavy Legs. From there I mix it up to One lower body exercise and one upper body (Quads/Chest or Back/Hamstrings or some variation of that).
I usually walk/run in the morning, lift at lunch, boxing/kickboxing/jitsu/wrestling after work.
Mixing it up is the key for me. If my lifting routine becomes a routine, it's useless to me. Mix in cardio and core whenever you can but don't overdo your core, it's just like any other muscle group.