I have a couple of MTI's programs, the Bodyweight Program, and Work Capacity Program. Both incorporate Progressions using the Leg Blaster Circuit, as well as Step Ups, Lunges, and squats within the Programs, as well as one day per week of running, progressing up to the longest run being 5 miles.
Here is a link to a Crossift Hero WOD involving Step Ups, that I regularly use in my own personal programming. I consistently get 1000 step ups in 60 minutes, so I no longer count the step ups, but simply set my watch for 60 minutes:
Sara Wilkinson and GORUCK present the hero workout "Chad", in honor of Navy SEAL Chad Wilkinson who took his life on October 29, 2018 due to the effects of numerous deployments, several TBIs, blast wave injuries and PTSD. Our goal is to honor Chad's life and legacy and by raising awareness for...
chad1000x.com
I don't find that step ups bother my knees as much as running. I regularly use high rep BW Squats (in the 1000 rep range), lunges, and step ups, to support my trail running missions, without the high impact and pounding caused by running.
Here is another link that may be of interest:
By Rob Shaul We’re continually evolving and improving our programming as we learn, get athlete feedback, and grow. We begin an intense 7-week Dryland training cycle with local athletes next Monday. Below are the changes I’m making over last year’s cycle, and why. 1) Training Eccentric Leg...
mtntactical.com
For backcountry endurance, Rob SHAUL is now also programming step up and trail running to develop boot packing and skinning endurance for the professional skiers that he trains.