When I switched tanks I transferred most of the removed substrate to the new tank, added some filter squeezings to it, then put fresh substrate on top - it was a larger tank. That was effective in jump starting the cycling of the tank. You can do a similar thing. I suspect you don't have the 2 to 4 inches of substrate that is ideal for plants, so you could just leave the "dirty" substrate you have and add enough of a new substrate on top of it to build up to the right depth. Then plant the plants, add water and add the fish back in.
From what I have read, a 54 gallon tank is too small for discus.