1. Definitely seek out professional advice from an expert in movement. Coaches can help to an extent with obvious faults in movement, but its almost always best to see a PT with background in the sport you’re trying to get back to (weightlifting, running, etc.) Rarely will you get an injury with just overuse while using proper movement, so having an expert to identify the source of the issue is best.
2. While recovering, modify movements to a range of motion where you don’t feel pain or modify your workout to achieve a similar stimulus. If your knees hurt while back squatting, try learning a low bar squat or box squat where there is less forward knee travel and hence less stress on the knee.
3. Quit with the “all or nothing attitude.” If you feel pain while running, don’t stop running until the pain goes away and then go do a running WOD that includes a mile of running. Start with 100m of easy running in warm-ups, once you can consistently do 100m runs without pain, increase to 200m, then eventually 400m. Gradual increases in volume is almost always the best bet.
4. Training around injuries is normally pretty easy. With minor to moderate injuries, there is almost always something you can substitute or modify. When you are training around injuries stop thinking about what you can’t do and make measurable goals to improve on what you can do.