Time to See a Doctor?

So I did a 35 min steady state run yesterday instead of my 20-25min HIIT routin because I was extremely tired after a round of midnight shifts. The run went very painfully (knees/hips) and I know my running shoes are getting old and close to needing replacement, but I am starting to wonder if my gait (under-pronating) is effecting my weight training as well. I was supposed to deadlift today but was too uncomfortable. I did back squats instead and also experience a lot of pain in my outer knees and right hip flexors. Anybody else experience anything like this?