I think that should be fine, but the best way would be to test it, which should be very easy. Wire one pin to another pin, set the first as an output so it can send a pulse, and then attach interrupts onto the receiver...
I remember Paul said that it is theoretically possible to have multichannel USB audio but you would need to do a lot of work with the USB protocol in order to do it.
If you only need a few khz, you could try doing it...
I don't know of a better way but I'm no expert. You could write a new envelope object based on the old one that takes an additional trigger input, which probably wouldn't be too hard, but the audio code can be pretty...
I don't think this is an audio issue. It seems like the SD card is failing rather than writing extremely fast. You would need to check the error logging from the SD library to see why. It might be because you need to...