Your post has so many questions and thoughts I hardly know where to begin. Can I just summarize your theme through the question "how you do you know if you are doing too much?"
The first clue is pain. Pain is always a no-no. Unfortunately pain is always a very subjective experience. Paul Grilley likes to use an analogy in the form of a spectrum. People in pain range from the Black Knight of Monty Python's Search for the Holy Grail to the Panda Bear. The Black Knight is one who may suffer a leg being cut off and claim that it is merely a scratch. These people don't react to pain in a healthy manner: they would rather ignore it and force their bodies to carry on. At the other extreme are the Pandas for whom even the slightest sensation is too much, invoking fear and anxiety. They may say something like, "I felt a something, you know? A thing. And I am not sure if it is a good thing or not but I don't want to feel that thing anymore!"
Everybody is different and their subjective experience of pain is also going to be different and on top of that is their ability to tolerate pain. But let's try to define unhealthy pain: this is any sensation that can be characterized as sharp, burning, stabbing, electrical or tingling. Generally these kinds of sensations indicate that the tissues are being damaged or are about to be damaged. On the other hand, dull achy sensations is generally what we want to feel in our Yin Yoga poses. We do ask a lot of our tissues and we need to feel something, but not too much. (See the Goldilocks' Position
article for more on this.)
Sometimes the pain occurs long after the yoga practice has ended, especially with nerve damage. Be alert to these pain sensations at any time: if you do feel pain think back to what you may have been doing over the last 24 to 48 hours and see if there is a correlation to the current sensations/tingling/pain and your yoga practice. If you can find a correlation, be extra cautious in your next practice and avoid going so deep in that area.
In the practice, any pain at all is a demand to back off or come out of the pose, but sometimes we don't have to wait for pain to arise. If the breath becomes short or choppy, you may be working too hard (in a yang practice) or beyond your edge (in a yin practice). The body's own wisdom knows when you are dangerously close to harming yourself, and in self-protection the body will tighten up. This tightening up is to reduce the dangerous stresses so that damage doesn't happen, but tightening up is the opposite of what we want in a yoga practice. We want to open up, but if you are too deep, you won't be able to open up.
Read the section in YinSights about playing your edges
for more on how to approach your limits safely.
Intention plays an important role in preventing injuries. Be clear with yourself about why you are doing the practice. Are you seeking maximum performance or optimal health? If it is the latter, then there is never any need to go past your edge in a pose or stay when pain arises.
For the super-flexible students, the intention is not more flexibility or more mobility, but rather stability. For these students there are still tremendous benefits to doing Yin Yoga: the deep calmness of the mind and the energetic benefits can be found even without going really deep into postures. Remember always, in Yin Yoga, time is more important than intensity. Just find an edge, it doesn't have to be a deep edge, and stay there. Even if the edge recedes, you can still benefit from the stillness and from the breath.
For students who are injured, it is good to mobilize and stress the wounded area but only mildly. It is a trade-off: we want to stimulate the damaged area so that healing can be assisted but we don't want to go so deep that we re-damage the area. I can't tell you how deep that is - the student needs to work with her teacher, her health care provider and her own inner guru to figure that out.
I hope this helps!