Welcome to the TRS community! Seems like you have a solid routine going! So to address some of your concerns.
For the ground pigeon and the knee pain. You may need to modify or remove this stretch from your routine for now if it is aggravating your knee. Try performing on an elevated surface rather than on the floor. You may find you can better control the intensity of the stretch better from an elevated position. To take the tension of the knee keep the knee bent to less than 90 degrees. The goal is to feel to stretch in the back of the glute, not in the knee. Also we are not big fans of icing an injury. It can delay the body’s natural healing processes. If you have a chance check out the latest video put out on icing (https://www.youtube.com/watch?v=0JflPw5FQEY). Try to find pain free movements and modify exercises in ranges that don’t aggravate the knee. Think slow tempo and controlled movements. Goal is to keep moving. If this issue does not resolve and its impeding your ability to exercise however may need to seek out a medical pro.
For the couch stretch in your TRS routine don’t worry about getting the torso all the way upright. Control the intensity of the stretch by first making sure you can keep glutes squeezed and modifying torso angle. You can start with torso more at a 45 degree angle and support with arms on the ground, again remembering to keep glutes engaged.
With sitting as much as you do the best way to counteract that is movement! The body doesn’t like to be in chronic postures. Try adjusting your position every 30 min or so, get up, move around, stretch, walk etc. Better yet try and get a standing desk.