if you were running Debian, I think the only thing you would need to do is change the command line to reroute the console (mostly - more on this below) to the other tty port.
Rebuild the kernel by following the steps here: http://releases.linaro.org/96boards/dragonboard410c/linaro/debian/latest/ When you get to the mkbootimg step change the command line from MSM0 to MSM1,
–cmdline “root=/dev/disk/by-partlabel/rootfs rw rootwait console=ttyMSM1,115200n8”
This will move the console to the other port, once the system is up and running you will be fine, but there is a minor issue. The early bootloaders will spit out messages on ttyMSM0 because you haven’t moved their console port. I think you can work around this by having the Teensy ignore all serial data for the first 10 or 15 seconds after power-on. Once the system is up and running everything should be fine.
Your HW solution is the correct long term solution. the short term solution of moving the console will be enough to get you up and running.
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