Keyboard and trackpad not working.
So, I just put the logic board from a mid-2012 MBP unibody into a mid-2011's shell. It booted fine, but the trackpad and keyboard don't work. Except to reset the SMC and PRAM. The keyboard works fine for that...
This person pretty much describes my symptoms exactly...
...including the flashing preference option.
The only suggestion in the accepted answer is to update firmware, but none of the firmware updates will run on El Cap. The App Store doesn't find any new updates.
Firmware sounds like a reasonable guess. The keyboard is clearly talking to the logic board since you can do the classic resets with it. I just can't figure out how to update that firmware.
Or maybe it's something else entirely.
Well ok, no bluetooth, I guess. Which is interesting, but I never use it, so it's not a loss, really. But on the other hand maybe that is also a clue. Or maybe not.