I capture 3 x 2 channel audio streams and save to a 6 channel file.
I want to use one of the 3, example the 2nd set, channels 3,4
something like channelcopy from 3 to 1, from 4 to 2 and only use 1,2.
And you want to export with only 2 channels. That is not directly available in Shotcut where you need to set it to 6 channels. You can export with 6 channels with the Copy Channel filters, and then run ffmpeg to drop the extra channels. Something like
ffmpeg -i export.mov -c:v copy -c:a aac -b:a 128k output.mp4
Notice, I used .mov for the export. I recommend to export as MOV because then you can set the audio to pcm_s16le or similar. You want to avoid multiple generations of AAC compression, especially using FFmpeg’s AAC encoder (future version 9.1 is supposed to improve it).
I’m creating my own .mlt, is there a plugin I can use?
No
Well, you might be able to use FFmpeg channelmap on the MLT avformat producer’s filtergraph property.
I have not tried it or used filtergraph on the MLT producer much.