That is a tough and stressful spot. I've been there, and lived to tell the tale.
Let me encourage you to not lose sight of why your spouse/doctor is doing what she does. Her practice goal is not to "maximize throughput"; it is to be the best physician she can be as she sees it. She is a physician, not an investment banker or an accountant, and there is a lifetime of training and honor guiding her every decision. jimmie, or Leslie, or I might visit your practice and say " why are you doing this part this way? You could make your life easier, if only..." But, for her that would not be true. For example after what seemed a lifetime of dealing with emergencies and ICU patients in addition to an outpatient practice, my spouse/partner and I decided about several years ago that we were either going to retire or find a way out of hospital work, night and weekend call. The answer was to support a group who became hospitalists. We gave up ER and inpatient care without a second thought. But there are some local physicians for whom inpatient care is so much a part of their image as a doctor that they could never do that. They had to find their own way, or eventually change their view or retire.
We survived medical training because we saw it gave us something unique and precious. It is also very fragile. I do not think it survives well when forced to be "efficient".
David Grauman MD Department of Medicine Commonwealth Health Center Saipan, Northern Mariana Islands