plx bear with my criticism... not trying to be a prick. I've had/still have all of your injury you have and I can help you. first i must address that there's no reason for you to be struggling with those issues. you already mentioned that its from going too heavy but its not like you're squatting 405lbs.. either you were taking wrong advice and/or you weren't warmed up enough(will get to this in a bit).
issues...
looking from the pic, i can tell you have some structural issues like tight hip flexors and lack hamstring development(explains the knee issue) and your traps need more direct work(explains shoulder issue and prob bicep as well on shoulder joint). It also seem like you need direct internal rotator work judging from your ability to expand your scapula(lat spread). neglecting any muscle group(even chest) IMO is a mistake, you just need to make sure all muscles are in balance in terms of balance to ensure you stay injury free.
why your joints hurt...
1. tight hip flexors basically shut down your glutes from firing. squatting/leg pressing require actions all 3(quads/glutes/hams) thats 3 muscles VS 2 or 1 muscles doing al the work. knees are taking a beating every time you squat.
2. lagging hamstrings. aside from visual imablance, lack of hamstring makes knee cap track froward when the knee bears weight like when you're squatting, torn patella can result from this. hamstring track the knee back in place and allows fro safe squatting.
3. lagging trap. traps are major stabilizer for every upper body exercise. some trainers recommend against direct trap work but I disagree. all the injuries surrounding wrist, elbows, and shoulder stem from neck issues and having enough muscles(balanced) in trap/neck is very important!
4. internal rotators. they assist in stabilizing shoulder joint and keeps the humerous in AC joint(keep from dislocating). ever do chest press and seem like one shoulder appears wider while doing a set? thats the symptoms of underactive subscapularis(an internal rotator). keep in mind front delt, pecs, and lats are all internal rotators as well.
solutions...
1. knee issue: start every leg session with foam rolling(work on quads, IT, piriformis, calves, hams, and spine in that order)then do intense leg curls. I prefer seated leg curl for this. 3 warm up sets x 15 alternating then do 4th set for heavy all out 15 reps followed by 2 drop sets of 10 reps(25% less weight each drop), then go back to the heaviest weight and do 20 1/4 reps in stretch portion of the exercise. alternate every sets of leg curls with stretch drill explained below.
stretch drill: take a long step froward like a deep walking lunge and place both hands on each side of leading foot. push your hips down and forward so you feel stretch on front knee, front upper hamstring/groin, and hip flexor in hind leg. now keep the hands where they are and attempt to straighten up front leg by lifting your butt up and back. you'll feel intense stretch on entire hamstring and calf on your front leg and feel the quad fire up. keep both feet and hands where they are and repeat 5 more times. then repeat other leg.
2. lagging hams: partially solved by leg curls... but now you must use them on squats and leg press. with hamstrings and hips loose, you'll notice getting deep on squat no longer seem difficult. keep the sqaut to parallel for few weeks then attempt to increase depth as your knees get better(they will). follow squats with leg press pushing on heels for more qlute recruitment. finish leg session with light stiff legged deadlifts to stretch hams out. calves can be done on leg day or separate days if your legs are shot.
3. lagging trap: hit all 3 region, upper/mid/lower. do your deadlifts and face pulls. also start every reps of lat pulldown with shrugging yopur shouler down first, then pull with elbows. i also recommend YTWL on incline bench facing down. many youtube videos on this...
4. internal rotators: simply start every upper body workout with a set of internal/external rotators, 20 reps each. then activate the target muscle with an isolation movement before doing compound(flyes for chest, pullovers for lats, laterals for delts)
how to keep muscles in balance, visually and strength wise?once your joints heal up, start ground level up, just like any hardcore BB's. that means building your legs, back, then shoulder girdle. strong legs will aid in strong back, which then aid in strong shoulders. consider low bar squats to keep chest open and neck/trap loose. deads and bb rows for proper shoulder alignment(think scapula) through trap/upper back development, which will support your pressing strength.
hope you can find these info helpful. you do have beautiful natural shape and you can do well in shows.