I know this has been asked a million times, but I promise, this is different. 
I have several recordings of songs that have five parts (guitar 1, guitar 2, bass, keys, drums). All the files are in stereo flac format. I have “practice” tracks for each one of the parts where that specific instrument is omitted from the recording. There are also instrumental, and instrumental + vocals tracks. I’ve been able to get very clean isolated channels by aligning and subtracting each part that is missing an instrument from the main instrumental track. However, there is unfortunately one song that gives a lot of bleed through of each part when trying to do this. I guess the instrumental doesn’t match up as well waveform-wise with the practice recordings.
By picking two practice tracks at a time and subtracting one from the other, I can get clean separation with pairs of instruments, but is there any way to narrow it down to a single instrument from this method? It’s not the worst thing in the world if this is as far as I can get with what I have, but it would be preferred to isolate each instrument. Thanks!