I assume it is pre-recorded audio? Ie. Not a sequence like MIDI or SNES format. If that is that case (its a format like .wav or .mp3 or embedded in a video) then a new-soundfont remix would be unfeasible, unfortunately. The song would have to be entirely re-made.
Edit. BUT if you have a midi file or similar it would be very easy! Do you have one??
Well, actually, you can convert .wav, ogg, etc to midi. Some ways take more work than others.
Simplest free solution:
Bearaudio Although, Bearaudio will not separate the instruments. Also, Bear is an online converter.
PaidMelodyne Studios: can do the same as Bear, but it is a paid piece of software. Not sure if it separates instruments. More at
YouTube.
AnthemScore: Same as Melodyne Studios, but cheaper price wise and it has a Linux version.
Similar paid software and price comparisons:
HereFreeBearaudio: Although, Bearaudio will not separate the instruments. Bear is an online converter and deletes your file after 2 hours and it can convert many different file formats. For instance, it can convert WAV, MP3, OGG, AAC, and WMA to MIDI.
Sonic Visualiser: It works on multiple platforms (I use it on Linux), but it takes more work than the others. It shows you a melody spectrum that one can trace on layers and export to Midi. It is a good learner tool. I used this to make opensource music into midi because sometimes their instruments suck, but their music is amazing.

Here is a
quick explanation by Hibou57.
AmazingMidi: This can turn a wav file into Midi for Windows.