Overcoming lingering bursitis/tendonitis

Last year, about this time, I failed to listen to my coach, who is much wiser than I, and over-trained my left knee to the point of crippling pain. I was diagnosed by my doctor to have bursitis and tendonitis after an MRI, and prescribed anti-inflammatories and rest. I have done this, along with a car accident in between, and continued to run periodically. I started with low distance, I'm talking 1 mile and working my way up by the 10 percent rule religiously, as to not have it happen again. I find myself still getting swelling in the back of my knee, if I run a short 2 1/2-3 mile distance. The discomfort is nothing like last year, but I recognize the feeling and back off. Cycling between runs helps, and causes no discomfort. How can I get my distances back without the swelling, or is it just something that I have to get use to. I rarely ice, but maybe I need to. Just don't like the feeling. Or, am I lacking stability elsewhere that caused the problem to reoccur. Getting frustrated.