you may find the AT injury is cycling related rather than running.
My adivce save the cash and stay away from anyone tellnig you to RICE a tendon - what a lot of crap.
Have someone look at your bike and cleat position, get back into walking and hiking before running so its not a case of nothing then something.
As for the shoulder - no idea but unless its really hurts, keep swimming, get stronger and you'll probably adapt adn the popping will go.
I know that when I have pain caused by weakness, such as sore knees when cycling, then the easiest and cheapest method of resolving these issues is to train and get stronger, amazingly the weakenss disappears.
Functional strength by doing the activity, rather than months of gym work and exercises just to lose specific fitness. Maybe I've spent to much time listening to Sutto...