It seems like you are already doing so much to prevent the nagging injuries, so sorry to hear you have this pain. I too have joint/tendon pain in my legs (knees mostly) and have found two long term practices that have reduced and almost completely eliminated the nagging injuries.
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First, would be to look at any potential supplements or healthy oils/fats that you may be missing out on in your current diet. As an endurance athlete and vegan for 10 years I am sure you are well on top of this, but would suggest this daily supplement if you are not getting sufficient omegas or inflammation reducing intakes. Omega Sport+®
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Second is a regular if not daily stretching/yoga routine. I’ve compiled various stretches from my physiotherapist, trainerroad videos, and other respectable resources to construct 30 routine that I try to do 5 days a week at a minimum.
I have recently been between apartments and not having the Omega Sport on hand has caused a return of knee pain, while my lack of stretching results in lower backpain within days, so I’ve been reminded recently of how important they have been for my injury prevention. For the oil, I don’t take it multiple times per day as recommended, just a small swig from the bottle before breakfast usually. Some people dislike the taste, so combine with meals/salads if thats you.