I've been playing around with this for a week now, so I thought an update might elicit some responses from someone. I have been trying to keep my arm stroke short, as originally planned, and the key thing has been to time it to my undulation. I am proceeding very slowly and carefully, because my main concern is not to re-injure my shoulder, and my technique is still in a state of evolution, but here are my preliminary findings.
I think that in my pre-injury fly I used to glide a fair amount in contrast to what I am now doing. Key in not injuring my shoulder is to let my shoulders rise up over my arms before exerting any force on the arms. To do this, I am using a much more active up-sweep in my dolphin kick, which shortens the period of my kick compared to what it was before. I think what happens is that this active up-sweep is in fact pushing my hips downward against the water, which then raises my shoulders in relation to my arms. As soon as my arms get in a safe position (in the scapular plane?) I can start my arm stroke without hurting my shoulder. As noted, the stroke is short, and it helps to go in up front with my arms wider apart, which means that the next down-kick will also come faster than in my old stroke.
In summary, my kicking frequency has increased to accomodate this stroke, but I have the sense that I am doing much more with my body and less with my arms, which is probably good for the shoulder.
Any thoughts, suggestions?