Effect of swimming on other activities

A couple days ago I was tossing a football and was dismayed to find that I couldn't throw it even 40 yards without shoulder pain (despite warming up for 10 minutes). I'm 43 years-old, and as recently as a year ago I could throw it 40 yards on a rope, and some 55 yards with no problem (no, I'm not the uncle in Napoleon Dynamite, lol). Granted I haven't been throwing much these past few months, which could contribute to the problem. I'm not having any pain swimming, and in fact can go much longer without stopping than ever before. It got me thinking about the effect of swimming on other activities, and whether I need to do some things to "counteract" or balance some of the effects of swimming. I do weight lifting on a bowflex and try to strengthen my back and rotator cuff muscles. I stretch my shoulders and pecs a lot. It feels like some swimming related muscles have become so strong and tight that they may hinder me in some ways. Any of you have similar experiences? Any exercises you recommend? If it is unavoidable, I still will continue to swim and live with any deleterious effects because I've fallen so in love with the sport and feel incredible after doing laps. On a positive note, while playing hoops I feel like my vertical jump has gotten a lot better. Must be the quads effect of all those kick sets.