You’re probably not going to want to hear this but it is most likely the running. It is very, very hard on the body, particularly if you are heavy (doesn’t have to be fat, could just be muscle from working out) and for most people it will take its toll on the body, particularly as you get older. If you haven’t already, go to a specialist running shop and make sure you are wearing shoes that are designed specifically for your gait, and potentially look at getting coaching to make sure you are running with the proper form which will reduce injury.
If you don’t mind switching to another form of cardio, look at low impact options such as swimming, cross trainer, rucking, eliptigo, rowing and cycling. The last two are particularly good, especially for home workouts, as there are really good apps such as Zwift, EXR, Fulgaz etc that make them fun to do. The science around FTP training is also firmly established at this point, and following along with an FTP plan will raise your fitness levels more effectively than just about anything else.
For recovery, there are all kinds of options. Sauna, cold plunge, myomaster, massage guns, all of these things do work. I’m personally not a fan of rollers and lacrosse balls and think they’re a waste of time compared to a massage gun. Vibration plates are a waste of time for exercise but are really good to use just before a yoga session and will unlock a bit more range of motion.
For yoga, I am a massive fan of the DownDog yoga app. You can substitute a warm up with 10 to 15 minutes of one of the more active yoga types they offer (and you can verify this by wearing a heart rate monitor and seeing if you hit zone three). For flexibility, I prefer yin yoga (long static holds) which down dog also offers. There is all kinds of conflicting information surrounding flexibility e.g some people say you shouldn’t static stretch and should only do dynamic stretches, some people say you should stretch with light weights etc. My recommendation would be to try things out and see what works for you. I personally find static stretching to be good for improving my flexibility and well-being. When you’re doing the poses, don’t be afraid to move about a bit and explore your body; small tweaks to your position can often have drastic effects in how effective the stretch is. This is especially important when you’re just starting out or doing a new pose you’ve never done before. I recommend doing it continuously though: as you get more flexible, you will often find that you will have to tweak your positioning to get the best stretch for your more flexible body.
For resistance training, get a few PT sessions to evaluate your form and make sure you’re doing things correctly. Do more work with sandbags, dumbbells and kettlebells and less work with barbells which are far more punishing on the body. Bodyweight stuff like the p90x you mentioned or weighted bodyweight stuff is also good. If you’re feeling twinges from your current split, look at switching to doing all body workouts or push/pull rather than hammering an individual body part in one session.
Also potentially look into getting your testosterone levels checked out by a doctor and potentially supplemented to bring them to the same level you was at when you were in your twenties. This will massively aid in recovery. If you feel hesitant about this, it is highly likely that the majority of fitness YouTubers, actors and whoever else jacked and over 40 is on HRT or steroids. HRT prescribed by a doctor is most likely healthy. Steroid use over and above your normal levels is most likely not unless you’be done your research and know what you’re doing.
Make sure your diet is good and you are getting enough sleep. Look at GLC2000 or another chondroitin supplement for joint health.
If you feel something twinge in a workout, stop immediately and avoid that muscle group for the rest of the workout. No pain no gain is for when your muscles are burning because of lactic acid buildup, not when they’re injured.