Arjuna performs surgery

Her bones began to flow like water under the guidance of your prana, reshaping and redeveloping into far more organized, intelligent structures which were far stronger and better at their intended tasks with the exact same material. Likewise her muscles melted within her body and reformed better, developed and corrected from their inferior and counterproductive states into truly useful macro-organs. Other specific organs were temporarily broken down and redeveloped for greater efficiency-the stomach and digestive system, the heart and lungs, the kidneys and liver-but that was just a bit of maintenance that ought to be done for everybody rather than anything special in particular. Your Alteration allowed you to keep everything functioning optimally while you temporarily shut down and recreated entire organs, so even the brief period where she literally had no heart was of no real concern.

As you expected you didn't quite have enough biomass to achieve total repairs in her body, so you had to cannibalize around a full inch of her height and compensate for the shrinkage to actually complete your treatment. Again, it wasn't particularly difficult more as time-consuming as you had to carefully work through each and every one of her veins and arteries to make sure that everything was properly arranged. The funny thing was that after total repairs you actually had a small surplus of biomass left over. Now how to arrange this...well, the human body was predisposed towards storing excess biomass as fatty tissue. She probably wouldn't notice a couple extra millimeters on her chest.

Finally was a quick biochemical tuneup in her brain to adjust for her increased physical parameters, a quick nudge towards specific receptors that would that would increase hunger to maintain her new level of energy consumption, re-arrange signals here and there so that the experience doesn't leave her with debilitating full-body pain (like it did to you when you first did this for yourself) and instead leave her with a feeling akin to laying on a cloud, and you're done!