Maybe just a difference in terminology, but I think you mean the z-switch (ZS), which is closer to whole stroke freestyle than "spear" switch (SS). Spear switch is done entirely underwater; in ZS, you bring your arm out of the water with the high elbow and spear into the water just right.
I have spent weeks and weeks just on drills leading up to ZS, and just discovered last week how to do rhythmic breathing in ZS / whole stroke. Along the way, I read and reviewed over and over, the TI books and dvd's, and explored the forum for advice. Each time through, I picked up some fine point or insight I had missed before; something that explained what I wasn't getting.
All I can say is take your time. For me, TI is "swimming as a martial art," learned by perfecting progressive drills one at a time, always cycling back, reviewing what was learned in prior sessions. I need to anyway, since TI is so dependent on balance and I find that even a 3# weight fluctuation can change my balance, so each day I start with a warm up of all the TI drills in sequence, so I know at the outset what I'm working with.
I was actually surprised and exhilarated to find that rhythmic breathing just clicked for me the first time I finally tried it, considering all the time I put in on the lead-up drills--I was beginning to think for a while that I would never swim. But maybe it was that patient time spent "perfecting" details that made all the difference.
I hope you resolve your shoulder problem. Maybe going back to drill basics will help, though it might seem remedial to someone who already knows how to swim. Or, perhaps, you could find someone who knows TI to watch you swim and figure out where your form might be off. Personally I can be a visual learner, so it helps for me to watch video of other TI swimmers and just do what they do when I'm in the water. If you don't have the Easy Freestyle dvd, it may be worth getting. If not, you can find many video's of TI swimmers on youtube, many of which I found referenced in this forum.