As others have said, diet is a pretty big part of controlling the way your body looks. And as someone above mentioned, a lot of that pain in joints type stuff will improve quite a bit once you actually start working out and building those surrounding muscles up. I actually really recommend you start doing that stuff now - if you have pain now in your twenties, I can assure you it will not get any better as you move into your 30’s, 40’s, and 50’s.
I also have a really fast metabolism, so I actually stay in the gym to keep weight on (pescatarian, so not a lot of “bulking” food in my diet). I have a sweet tooth, but almost never drink soda, and don’t buy a ton of junk (yogurt and fruit can be decent late night snacks, for the record). I’m lean, but in pretty good shape, and work out primarily because I’m vain and women generally prefer a man who’s in shape
My workout below:
10 curls each arm (with a weight you can curl w/o “swaying”)
25 push-ups
25 dips
x3
25 straight crunches
25 push-ups
24 side-to-side crunches
20 shoulder shrugs
24 side-to-side crunches
20 shoulder shrugs
That’s my “standard” workout, done basically like circuit training where I go from one exercise immediately to the next one. It actually doesn’t take very long - maybe 30 or 40 minutes depending on motivation.
My leg day workout is:
15 kettle bell squats (I use 80 lb dumbbells for this)
24 side-to-side jump squats
25 leg curls with a giant exercise ball (works hamstrings)
25 push-ups (hey, I said I was vain )
x3
25 straight crunches
25 push-ups
1 minute side plank
20 shoulder shrugs
1 minute side plank (other side)
20 shoulder shrugs
And I’ve begun biking 3-4 miles in high resistances as well every other day.
Big thing to remember is that your workout should be tailored for you though, and that workout consistency counts for a lot more than workout intensity. You don’t need to kill yourself working out - just be consistent and do enough to give yourself a good burn. You said the side crunches are a no-go, and until you get your wrists feeling better you’ll probably want to do an alternate form of chest than just mass push-ups, but the above should give you at least some ideas about how you can construct a decent full body workout. You don’t need to pump a ton of iron or anything; a good selection of calisthenics can actually hit most of the areas you said you want to work on.