Tony,
it sounds like your knee is pretty rough shape. if you've had good results with the PT exercises you did previously, and you think your knee is that weak, i'd redo your PT exercises again for several weeks. after that I'd integrate some of those exercises into the corrective phase.
I had shoulder surgery in february, and although it's been in decent shape recently, i added two additional PT exercises per workout during Phase 1 to strengthen my external rotators and upper back. even during Phase 2 i'm doing additional rotator work.
The S2B program has you moving some decent weight so i'd spend additional time up front to get your knee back in order rather than have to sacrifice weight and/or time later in the program.
good luck.
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