I suspect you know what your doctor will tell you. The urge to continue to train is well understood by users of this forum, but I think all would agree to give you permission to stop training until this issue is resolved. It's OK.. We get that you are highly motivated, and definitely not a wimp.
While it is fairly well known that certain benign forms of muscular soreness can respond well to the circulatory benefits of continued exercise,The old adage "listen to your body" applies here. If it does not seem like the usual muscle pain with which you are already very familiar, it probably isn't. I agree that increasing pain during exercise, and intermittent pain at rest, are not good signs. You have been very observant and your account is detailed.
Though length of down time is an important factor for determining how long it will take you to regain your fitness after you solve this recent issue, the amount of time you spend running through pain can set you back much further than rest time. To put it another way, trying to exercise until your doctor tells you not to, makes it seem like you have no control over your health and fitness, and you certainly do. You have the primary responsibility for putting on the brakes when signs point in that direction.
One metaphor for what may be happening involves an understanding of diagnostic imaging, and the diagnostic process itself. For example, it takes about 8 years for a cancer to develop to the point that it can be detected by conventional means. Another example is the typical stress fracture: not visible until calcium deposits begin to form. In other words, waiting for a concrete diagnosis can be the same as waiting until it is too late to reverse the condition you fear. Anybody can have 20/20 hindsight. You want to develop the ability to ameliorate problems before they develop out of control. This recent setback is a concrete example of that.
I think it is useful to view recovery time as money in the bank. The interest may appear small, but it still accrues in a positive way. Running injured, on the other hand, is like a payday loan. The interest is much higher, in a negative way. Bottom line is, you will get better overall results by undertraining, than by overtraining. You can always live to fight another day.
Regarding any techniques for self-diagnosis, I think you have offered an abundant amount of evidence for any competent physician to use, so your efforts to muddle through have not been completely wasted. Sometimes people give up too early, and it puts a lot more pressure on the doctor to come up with a solid diagnosis. However, there are diagnostic tests that can deliver most of the same knowledge as the school of hard knocks, in less time, with less potential damage.
I'm not sure which bone you feel pain in, but I'll assume from your mention of "shin splints" it is the Tibia. The anterior/medial surface of the Tibia has no muscle, so pain from pressure on the bone is often assumed to mean a bone problem. Fair enough, but there are plenty of places on the human body that are sensitive to touch without any injury present. If you checked the same spot on the other leg, and it was not as sensitive, there is a better chance you are on to something.
However, tissue near an injured site often has enhanced sensitivity. There could be portions of the periosteum covering your bone that are sensitive due to damage or inflammation nearby. Your sense of depth can be quite misleading. For example, a strain where the rear calf muscle Soleus attaches to the bone might enhance sensitivity to pressure along the adjoining Tibial bone surface. Similar pains can occur on the Fibular side that feel, for all the world, like a broken bone. Some rear calf muscles will produce pain in the vicinity of the Achilles tendon that feels like tendinitis.
If scans continue to show nothing major, it may not be the usual muscle problem, but a new one. Yes, muscle problems frequently feel like they are deep within bone. The perception of pain is a mental construct that approximates a 3D image of what's actually wrong. It isn't perfect information, but useful in that it gets people (most people) off their feet. That's what "listen to your body" is all about. It may not be accurate, it may be teenage histrionics, but it (usually) works.
So, my advice is to take a real break, so to speak, get off your feet, and keep probing for specific symptoms, locations, and actions that will help your doctor form a better diagnosis. If the tests still come up empty, your body may just have become very convincing when it comes to warning you of overtraining, which in this case would probably be a healthy adaptation.
