Marty Gallagher wrote an article you might be interested in
here.
Couple that with some kind of press and pull up and you're all set.
As far as cardio goes, I don't know if it's a good first priority for someone getting back into shape. The program in the article is a mix between strength and strength endurance anyways. My advice would be to build strength and enjoy the dramatic increase in work capacity that comes with it. Once you're body is strong, then add the cardio stuff.
Even if you go another route, there is one thing that you need to be careful of. In your case, with herniated discs (lumbar, I assume?), you have to be very careful about "butt winking." That is, letting your lower back go from neutral to flexion at the bottom of the squat. I can almost guarantee this will aggravate your discs. One reason I suggest working of strength first is that it's very difficult to maintain a tight, neutral spine while you're fatigued.
I suppose you could do some A+A style squats at the end of your workout for some extra conditioning. While not as good as swings or snatches, that's probably the safest way to develop conditioning with squats for someone with a back injury.