Just my two cents worth. I've worked with stronglifts. I've done several runs of the madcow 5x5. Currently I'm running a 5/3/1. Having said all that, I must agree with BtB, that stonglifts is an awful lot of volume on squats. However, since you are not doing free barbell squats now, perhaps that approach (IF DONE BY THE BOOK - STARTING WITH THE EMPTY BAR AND MAKING SMALL INCREMENTS NO MATTER HOW EASY OR HUMILIATING IT IS) might be a good place for you to start. There's not a lot of love for stronglifts here, but I think it DOES have its place. Good for a raw beginner for a couple of months in order to groove the form and build a solid foundation. Don't worry about getting your five sets of five every time. If you get 5x5x3 plus 5x3 plus 5x3 one day, try to get 5x5x3 plus 5x4 plus 5x4 the next time. One more pound or one more rep is still progression.
You're going to have a tough time on the 5/3/1 without doing squats. Perhaps you could substitute leg presses, but it really isn't the same thing. I'm not trying to discourage you, but I'm just saying that 531 is a solid routine, maybe not for you right now though.
The madcow 5x5 is something I use after I've had a long layoff. I like it because it uses five progressive sets of five reps. You're still squatting three times a week, but it follows a Heavy/Light/Medium (H/L/M) format.
My short, pointed answer to you is this. 1) Get your back issues resolved. 2) Do stronglifts until you burn out (It may take 2 months, 4 months, whatever), but do it BY THE BOOK - empty bar and all. You're building a foundation here. 3) Progress to madcow or some other 5x5. madcow is pretty easy on the body though. 4) After you stall out and reset two or three times on the 5x5, find another program or make your own.
None of what I said will ever get you a big bicep peak or razor sharp abs. It will make you hungry as a horse though, and if you eat right, you should be big and strong someday.
Good luck to you!
Bogdan Petia Sarac - Must keel moose and squirrel
Cancer Survivor - 7/21/10
Benchmark 5K time: 27:45 (3/5/11)
It's not the weight we move, but the people we move that matters. -- Bearded Beast of Duloc (12/31/10)