For your hands, pay attention to how you take your grip. If you take hold of the bar in your palm and it rolls out toward your fingers the skin scrunches at the base of your fingers and causes more irritation. If you pay attention to how this works and grip the bar more with your fingers and roll back into your hand, there will be less of a skin pinch and less irritation/calluses.
I have to warm up reasonably well to avoid knee issues, much more so now that I’m older. Generally, I try to walk for 10 minutes or so to get the blood moving, then ideally do some rolling and stretching. Sitting in a paleo squat (hold on to a rack or whatever if needed) for a couple minutes before squatting seemed to help considerably when a knee was acting up a few years ago. I start with bodyweight squats for 15 reps (usually while wearing a hip circle). Then only the bar for 10 reps. Move on up from there. My knees don’t like squatting without some foreplay, but with it they are presently doing ok.
Pay attention to your feet, which are very important. You want to establish and hold a good foot arch (this requires focus and effort). Knees should track out over your toes without arches collapsing. Don’t squat in squishy shoes. Also, how deeply you squat matters. Video yourself squatting. Ideally you want to go about parallel, but you don’t want excessive buttwink, shifting or other issues, and you mostly can’t tell what is happening without video of what is going on. I don’t "box squat," but I’ve been using a box to squat to as a depth gauge as I’m working out an uneven hip issue. I just barely touch the box. Really, video all of your exercises. What you see might surprise you. It did me. Is the bar level? How is the bar path? Anything else funky?
Regularly doing a lower body stretching routine helps. My adductors are tight on both sides. So are my hamstrings. I also have tightness in my left quadratus lumborum, piriformis and other things on that side. My left ankle/calf is more limited than my right. Everyone has weak gluteus medius muscles, so do some specific strengthening exercises for them. Knee issues are often from muscles well above the knee.
Rest time between sets depends on what you are doing. For muscle gain, a little longer than you are probably inclined to think is better according to studies. For strength, much longer is better. Power lifters doing heavy, low reps spend a lot of time resting between sets. But we aren’t power lifters. IMO, rest enough to feel recovered enough to do the next set. One alternative, which I’d often do to speed things along is alternate exercises. Alternate sets of bench presses with rows, or OHP with chin ups. Or whatever combos you like. You can also do "giant sets" of more exercises.
You mentioned shoulder and elbow problems from bench pressing. Be careful with benching and push ups. They are easy to do wrong in a way that screws you. You want good form with the lats engaged. It’s safer to shorten the range of motion, as in stop the bar a few inches above your chest instead of touching (similar for push ups). You won’t lose much effect from that and potentially stave off shoulder problems.
I’ve only read back a few pages of this thread. You are working on correcting back curvature. In your shoes I’d probably avoid bench pressing entirely for now and focus on push ups, again with good form - very important. Slow, good reps. Work up to say 30 or more good reps of push ups, then consider bench pressing if it’s what you really want to do. Also work on core exercises. Planks are good. When you get stronger at basic planks, add some side ones.
I don’t know what equipment you have. A power cage is very useful and IMO the best for a home setup. A modified cage is what I use. Don’t bench press or squat without a safety mechanism that you can trust.
I think you said you’re doing Romanian deadlifts (RDL). If/when you start doing regular deadlifts, you probably don’t want to start completely from the ground. I don’t have enough flexibility to lift properly from the ground with standard size plates. Many people don’t. It depends on body proportions and mobility. Use a low setting of safety pins in your power cage or, as I do, jack stands to raise the bar.
For RDL and squatting instruction, Alan Thrall is good. You can’t dislike the guy. Alan Thrall - YouTube I don’t know if you are squatting high or low bar, probably high. There is a difference, so choose instruction accordingly. There is also squat university: Squat University - YouTube