If you knew roughly what the illness was then it would be easier to determine the cleaning method - but if you're unsure then it means a complete strip down to be totally sure the setup is safe.
You'll need to wipe out all life including the life in the filter and in the substrate. Sorry.
Do you have any local fish stores or fish forum people that you could swipe some old filter medium from in order to save waiting for the cycle to complete from scratch? If so then you could halve the effort and worry.
If you do decide to wipe the set-up clean and start afresh, you will need to remove all living creatures (deal with these as you deem worthy - e.g snails can go out to the birds - at least this allows some benefit to nature) from the setup and empty the whole thing. Put your gravel in a big bucket filled with a hot mild bleach solution (bleach and hot tap water - keep a window open to save you from the chlorine!) - this will kill off any nasties - be sure to stir the stones to make sure they all get a dose of the bleach. Rinse with warm water until the smell is mostly gone.
Empty the water from the tank, Again- use a bleach solution to clean the inside of the tank and all silicone joins carefully. This is a good opportunity to polish out any inside scratches and get all the hard algae-spots off the glass. Rinse the inside of the tank well.
Discard all filter foams and clean filter ceramics using boiling water - Not sure how filter plastics would handle the heat..... best warm the water carefully and keep an eye on whether the plastics are changing shape.
Clean the inside of the filter with bleach solution and soak the hoses in as hot a water as you can get out of the tap. Above 60degrees kills most nasties. Replace with clean hot water once at least.
Then put the setup back together. Soak substrate in about 3 inches of warm water with lots of dechlor! At least 4 x the normal amount. Do this twice to be sure the substrate is clean of chlorine. You should now be able to start setting up as a tank - going through all the normal procedures and processes.
Good luck - sorry for the long instructions
