Given everything you said OP, I would expect a majority of people to be hesitant to give you advice. People feel the most comfortable giving advice when they can relate to certain experiences.. given your very unfortunate history, oh and by the way - You are one tough bastard, not many people will be able to relate or feel comfortable giving workout advice.
I'm included in the above group, however, there are some general advice that floats around in every thread.
1) You have pre-determined rest periods. That is, IMO, illogical. How do you know how you are going to feel on wednesday 12/06/2013? You don't. So how do you know how much time you need to rest after a 'shoulder press' set? You don't.
Feel it out. Do your set, wait until you "feel ready", and do your next set.
2) Squatting is GREAT.
Doing something that hurts you or injures you is the OPPOSITE of great. So, squatting for you is not great.
You don't have to squat. Just like you don't have to beat women and swear but some people will say you are a huge pussy for not doing it.
Who gives a fuck?
3) Your total program, again IMO, is not something that you should use. I think you should go with something pre-conceived.
A push-pull-legs routine. It still fits your 3x frequency, and it dedicates a whole day to your legs.
Given that you can't squat, your leg development will take a hit, right? Yes, it can, but it certainly doesn't have to. You just have to pay EXTRA attention to your legs. I think a dedicated leg day will help you do that.
Now, at this point of my thought-process is where the dilemma(that i prefaced the advice with) comes into play.. Even though I want to help a fellow person who is inspired and motivated by exercising, I don't feel comfortable suggesting what exercises you should do, or even what rep-ranges you should consider.
Perhaps, you should consider going low-weight & med-rep(5-8) until you actually get back to a 3 month stretch without interruption or injuries.