The squat is the only weight training exercise which I do for high reps, I go for 20 reps with the squats... Everything else I do is within 5-12 rep range.

OP, if you are having shoulder problems go for a deep catch on your freestyle.
I also recommend wearing short fins using a soft kick to take some of the burden off your shoulders; and focus on using your core and hip rotation to provide power not just yanking your arms through the water.
Kicking dolphin on your back also develop abs/back. Hands by sides uses different muscles than hands overhead.
Even bad shoulders and knees can usually tolerate a breaststroke variation using a single dolphin kick instead of the frog kick.
Do some rehab-style work with very light weights to strengthen all the little rotator cuff muscles that stabilize your shoulder. Stretch after warming up.
Don't do anything that makes your shoulder joints hurt. This may mean that bodyweight exercises in the gym are out.

Here's a good resource for rotator cuff rehab:
https://www.irongarmx.net/Articles/7_...f_solution.pdf

Thought I would post a follow-up. Had a fit issue on my winter bike after changing saddles, fixed this and is much better. Stopped swimming. Doing yoga twice a week for 6 weeks. I've need felt so good. Went for a massage yesterday and the MT was shocked that I'm so much looser. I'm pulling off 2.5 hr bike rides from far less and feel great.

Strength: Starting Strength.

Mobility/flexibility: Circular Strength Training. Check out Intu-Flow and Prasara Yoga.