Lots of unknown variables to give any meaningful advice.
My first question would be how active have you been in golf since the injury layoff? What is your age (as in, if you're not meandering into your AARP years - is it out of the question that you're not going to recoup your prior athleticism and swing speed)? Do you still experience discomfort swinging a golf club despite the surgery? Could the layoff and the time away from the game (for several months I'm assuming) be part of the reason why you're not yet experiencing your typical swing speeds? Or, perhaps, you're now trying to soften your swing to alleviate the stress on the repaired shoulder as to avoid further issues down the road?
You need to sort out the whys before you can graduate to the hows.
You very well might need a softer flex shaft, but it would be a shame if you change out those shafts, then next season you regain your swing speed and realize that those shafts can't handle the load you put on them.
Sometimes after an extended layoff, especially if we're not playing as much as we did in the past, we experience higher ball flight with more side/backspin simply due to swing plane and mechanics.