How can I strengthen joints, bones, ligaments etc.?

You may have underlying conditions which are now showing symptoms. First have an overall physical from a licensed physician. Lab work included! Your genetic history is important; heart conditions, auto-immune disorders, and much more. Other things to consider are age, gender, stress, type of exercise, balanced diet is too vague. Consider speaking with a Nutritionist so you are getting exactly what YOUR body needs. Weight training is very important! If you are female don't worry about "bulking-up" because your hormones don't normally promote that, basically you will notice muscle definition, strength, more range of motion, and overall strength increase. Hormones can be a factor but to get accurate results, ask for a saliva test and at different times of the month. Hormones fluctuate too much for a blood-drawn test. FLUIDS! With a little research your fluid intake is determined by your weight, overall health, activity level. Consider time with a personal trainer! Everyone has different needs and issues that effect a positive outcome for you; more reps with lower weight or heavy weights and less reps. Another suggestion...WEAR PADS! Sounds like you might have bone spurs (little pieces chipped off) which can be very painful. Trust me, take it easy on your body. I live with chronic pain, every day for the rest of my life. I'm only in my 40's and have always enjoyed very physical activities. Establish a positive health care support team.