I emptied my tank of everything but left the substrate in place but it seemed to work and I haven't had any since (years ago now), but I probably caught it really quickly!
Going to all that effort I would change the substrate as well as it probably needs changing anyway/soon and the louse or eggs could be in the substrate hiding, would be madness not too change it really if you are doing all this work anyway. Obviously don't put boiling water into an empty aquarium as it may crack the class? Like shrimp the eggs are carried around by the louse but some may have dropped? Completely emptying the tank, thoroughly cleaning/drying the glass and replacing with new substrate should be enough, I would quarantine the plants though to make sure there aren't any on those, well anything that is going back really.
As JayC says, you can use a bucket, or any other clean, plastic container! I think I reused the water from the tank as well pouring it through a fine net, then wash the net in boiling water once finished!
If you want to be doubly sure, you could put some carbonated water in the tank once you have cleaned it all, deep enough to go above where the substrate line was and leave that over night, then empty that and dry it thoroughly again before starting the new setup?
On the plus side, once re-setup that is probably the biggest job done for many years to come.
Simon