Wouldn't an easier way to do this be to control diet? For one thing, it slows the process of change down which would ease any shock-related side-effects. Of course, it takes a lot of work from the patient to adhere, but if they are at the point that they are considering fecal transplant, they're probably ready.

This also gives the biome a chance to adapt to anything particular about the individual, if possible (certain pharmaceuticals may not be able to be worked around.)

Also, I would think if you did the transplant and never changed your diet, you'd often just go back to the old biome after a time, but I could be wrong about that.