[lordvader]

I did copy the bootcode back to verify, and it definitely isn't working.

For the time being I'm using 3.1.5, with the bootcode from 3.1.3.

Also, let me clarify. A stock 3.1.5 install works fine. As soon as I alter anything in the /storage partition the Pi will only boot with the older bootcode.

OK, so I can confirm that my RPi doesn't boot with the bootcode.bin file that's bundled with the 3.1.5 release.
Using the bootcode.bin from the 3.1.3 release, I am able to boot, overclock, run of USB, and all the other awesome stuff.

Can you try copying the bootcode.bin from the 3.1.5 back on just to be sure.
It seems more likely bootcode.bin got coppupted in the upgrade, than it's incompatible with your pi
(there would be a lot more reported issues if that bootode.bin was incompatible with a specific board revision).