Quick update - had the initial appt for my knee this morning. Turns out the knee doc is also a shoulder guy so I got both done at the same time. Diagnosis:
Knee: bursitis - potential torn meniscus
(some detail:
http://orthopedics.about.com/cs/meniscusinjuries1/a/meniscus.htm). Have an MRI scheduled for next week. If it is actually torn, then arthroscopic surgery may be the solution. In the meantime, got a ref for a physical therapist basically to learn better / which exercises I can do to not annoy it further.
Shoulder: tendonitis in the rotator.
Got a cortisone shot and prescribed 2 Aleve x 2 / day for the next 2 weeks. Also told to visit the PT for some better / supportive exercises that won't hose it up further. I go back in a month or so and see if an MRI is necessary. He thinks it probably isn't torn - that would most likely be due to a specific trauma incident / injury and (luckily!) haven't had that. So mostly like just an instability / tendonitis.
So in the near term, I can train light and do cardio. He suggested against things like lunges & deep squats due to the stress on the knee... Ugh. Guess I'll have to find a good sports-oriented physical therapist...