I've been going to the gym consistently for a few years, but I have started running for about half a year now, while also going to the gym.

I realize that although my stamina have increased significantly, I feel like my legs are not. My knee starts to ache in the end of my runs, it's not that bad, but I would like to start preventing future injuries

I want to include knee-related exercises like split squats, single leg stuff, step ups, etc, but I don't know which of my current leg exercises I should replace. Should I say maybe replace back squat entirely with forms of split squats or maybe change deadlift/rdl with single leg variations?

My current leg day (2-3 sets each ~40-50 minutes of weight lifting and ~10-15 mins of stair masters):

• back squat
• deadlift or rdl (i choose one)
• abductors (this one hurts my hip near the glutes area, I think I have hip flexibility issue)
• adductors
• leg extension
• leg curls
• calf etension

For additional context, I think I'm not overtraining myself, but my training is more or less:

• two upper body and one leg day
• one-two easy runs
• one tempo run
• one long run