I would think changing substrate would be more fuss with fish to worry about. You might have to get them situated in buckets.. unless I'm just not thinking of another more clever way of thinking about it.
..Yes the 3rd phase really tries the patience because you feel you've already learned a lot about patience during the nitrite spike. Its one of the few exciting moments during fishless cycling when the N-Bacs catch up and the nitrite drops to zero in 24 hours and you begin to get zero nitrite at each 24 hour test. It makes you feel the end -must- be near. But then there's this one more unpredictable stretch that can either go quickly or can exhibit "the sticking problem" which is what I call it when that last little bit of either nitrite (or sometimes, surprisingly, ammonia) just doesn't quite want to clear at the 12 hour test. If you have a long wait for this, it sometimes makes for yet another exciting moment when -that- last problem magically clears one day. And I'll tell you, as one who has long ago carefully watched that last transition and the getting of fish.. I kept testing and testing and it was kind of amazing how those traces just never came back. Once the biofilter established itself it just kept producing true zero ppm readings for ammonia and nitrite for more than a year. I finally saw some traces of (I forget, a tiny bit of either ammonia or nitrite) once when I was pushed and unable to get anyone to care for the tank for a long period and I had skipped some cleaning even before that (a good gravel clean large water change fixed all that up however.)
All of the basics we talk about in our beginner section here have continued to prove themselves to me over time: the fishless cycle itself, the weekly gravel-clean-water-change and the periodic (monthly, to begin with) filter clean. These three things are just amazingly powerful tools for keeping a successful freshwater aquarium.
~~waterdrop~~