When cleaning all of the equipment, use a bucket of hot tap water with a cup or two of vinegar, then rinse thoroughly and let everything dry completely, including the insides of the hoses.
Nothing will survive it: Parasites, bacteria, etc. What little might survive the heat or super low pH of the vinegar solution won't survive drying out. A thorough rinsing should negate any problems from the system being previously medicated as well. If you are worried about it, run a polyfilter in each canister during your cycling.
Oh yeah... and discard all media... bio balls, filter pads, carbon, etc. Use all new cartridges and media.