My Knee Makes Itself Known

My knees used to give me all kinds of problems. The pain started when I was fitted with super stability shoes for my "over pronation" complete with hard-as-rock orthotics for my sky-high arches. Question - how does one pronate with stiff, high arches? Is that even possible?
The answer is basically no. I don't over pronate - however, my shoes wear on the inside because I have bunions (ew!) so I naturally land and push off on the inside of my forefoot. Because of this wear pattern I was given stability shoes twice at a local running shoe store. I developed constant knee pain that was so bad it kept me up at night and eventually sent me to the doctor. Unfortunately, he didn't really pinpoint the problem. He recommended I replace my shoes and again I was sold stability shoes. The pain worsened and ended in either severe bursitis or a ruptured bursa (I was undiagnosed because, you know me, I hate going to the doctor. But my knee swelled to the size of a grapefruit and the black-and-blue swelling stayed for months!).  The pain limited my running, but I put a few miles in, still feeling it. I stumbled on the fix myself when I realized that the more worn my shoes were, the better I felt. I switched to light, flexible, neutral shoes and almost instantly noticed a difference. In weeks the pain was history. 
Since last spring when I made the shoe switch, I've run a lot of miles and a lot of races. So far, no pain. I am leaning more and more toward lighter and thinner shoes.
This week, however, I felt pain in my right knee while running (my old injury knee!). Of course, this pops up right before a marathon! But this pain baffled me. It was a bruised, tight feeling on the inside back of the knee. It didn't feel like a running injury, but I couldn't think how it could have happened. I was blaming work. I blame work for all my problems, though, so no surprise.
Finally, the cause dawned on me. Remember my calf cramp during The Wall 30k? Running through it made me land all funny and hurt my knee! I tested this theory by clenching my calf muscle and running on it...sure enough, major pain in my knee area.
My plan? Well, I dialed down the miles last week and plan on keeping it light this week, too. I mean, I'm supposed to be tapering anyway. Haha. As if my life isn't just one big old taper! Tonight I'm skipping my run and going to a class at my gym that is hilariously entitled "Hard Bodies" and is taught by one of my customers. If he nudges me about missing classes, I scathingly ask when he last refilled his cholesterol drugs. Just kidding.
The good news is that the pain seems to be on the wane. With any luck and a little rest, I think I'll be fine for next Sunday's marathon.
Have you ever had a knee injury? If so, how did you deal with it and how long did it take to heal?