Also, I don't know if it would be possible. but replacing data on the rom through injected an edited midi could result in the song being played on original hardward, no?
What game are you importing to? It shouldn't crash the game.
What you want to do basically is remove certain channels from songs I take it. If so there is no easy or automated way to do that as there are a variety of sequence formats. If you have a decent amount of knowledge in reading sequence formats, and hex editing you should be able to go to a channel starting offset and simply put a end track flag at the start. That would "mute" it. If you're not sure how a sequence format works, there is a export "debug file" option in N64MidiTool that allows you to export a .txt along side a midi and that will give you a general understanding of the sequence format (type 1 sequence formats do not have this option eg: RareWare games). From there you could find the channel offsets, export that sequence as bin in N64MidiTool and hex edit the channel you want muted with a end track flag at the starting of the channel, then finally re-import the bin. Doing this will insure that you're not losing song information as midi cannot translate / import special commands. However, if it is a game that uses type 1 sequence format, it should be safe to export as midi, mute channel, then re-import.
It all sounds a bit tricky but this would be the only way to do what you want to achieve.
I'm using SEQ64. I managed to get the songs to play, but it crashed at 15secs in. I thought it might be pitch bend, but still looking into it.
I export the midi, edit it to remove the notes I don't want to hear, and export the midi back into the rom with SEQ64. It changes the formatting slightly due to the SEQ64 optimization process. It play with the notes missing until Project64 crashed at the same time.
I'm only using first- party game for now. Working with Mario Kart 64, Luigi Raceway at the moment. Project 64 crashed at 15seconds when the 2nd section of the song starts (bass line pitched bend down at this point). I removed the notes that pitch bend and it still crashed.
Will tinker around a bit more today to see if I can find why it crashed.