As a fellow Mr. Glass, I can sympathize with you. I have a seriously torn up back with a doctor-verified 65% disability rating, my right knee was torn up by a bull at a rodeo but never fixed, and my shoulders give me fits from time to time. But alas, there is hope and maybe I can share a few things that have helped.
For starters, I just can't push lifting hard all the time. Really long cycles run back to back leave me crippled for weeks somewhere along the lines. But I've found that I can train in the 75% to 80% range year-round. So I spend long periods working with moderate weights and building my base of strength and conditioning. A couple of times a year I will peak to heavier weights to test myself and see what kind of progress I've made. It's a much slower process but it's what I have to do to stay healthy.
The other thing that has saved me is focusing more on reps rather than just the weight on the bar. I get hurt far more easily when I get too close to my 1RM. But if I keep the intensity lower and just keep working on rep PRs (either with 5/3/1 or my current set-up), then I can keep most of the injuries at bay.
I've recently found Paul Carter's blog, lift-run-bang, and I've noticed that he talks a lot about the same kind of stuff. He doesn't really use it for injury prevention but he thinks it's a very productive way to train. You might want to check it out if you haven't already.
Lastly, listen to your body and back off when it doesn't want to give you what you want. Be conservative with your weight jumps and pick exercises that fit your style and needs. For instance, I box squat a lot because it keeps my back healthy. I think regular squats would be better for my maxes, but my maxes don't matter when I'm laid up in bed for weeks at a time. Find the lifts that fit you.