I just rooted my FTV yesterday with the hardware root. Unfornately I was already at the most recent firmware. Link2SD did not work for me, at least not automatically.
In the end I managed to get it mounting automatically. If anyone struggles the same as I did, here is my short Howto:
Scripts set up like here
I used "Amazon FireTV Utility App" to get the scripts on my FTV, shouldn't make a difference.
And you'll need Tasker! (Might work without it, but I didn't test it)
After you've completed the steps in the mentioned post, and I mean all of them, you start Tasker.
You create a new Profile that triggers on startup. Then create a new task for that.
First action should be a timer (wait or similar), 2 minutes should do it. If anything breaks, this buys you time to disable Tasker and prevent a bootloop.
The second action has to be Code->Shell. The command has to be:
umount /storage/extUsb/.android_secure && umount /storage/extUsb && /system/etc/install-recovery-2.sh
Mark run as root as well.
I've set the timeout to 20 seconds. In case something hangs it will just be cancelled.
Then do a restart.
After a little over 2 minutes a popup will ask you to allow Tasker Root access, shortly after that the USB connect message will pop up and then you can check in Link2SD whether it has worked.
If you want you may now lower that 2 minute wait. I've set it to 30 seconds now.
My guess why the scripts alone weren't working is that Amazon blocks every other USB drive when mounting. Might be, that they even unmount the drive.
Mounting my ext4 drive manually with "su -c /system/etc/install-recovery-2.sh" worked most of the time, but then FiredTV sometimes crashed completely. When manually unmounting the USB Drive from the ATV Settings the mounting worked perfectly. So I tried unmounting "/storage/extUsb" first, but my FTV wouldn't allow that. The device was busy... It took some time and a "mount" without parameters to see the mount of .android_secure inside the other mount....
Long story short: It may work if you put the two umount commands into install-recovery-2.sh, but I didn't try that. It might very well interfere with the AFT boot procedure and leave your AFT unusable.
Hope this helps somebody.