I've got the wires soldered to the back of the original board
Can you post an image of your hardware setup here that shows the wiring?
I've even dismantled the plug on an old SNES controller with a cracked housing and run jumper wires from the controller wires to the ControlBlock, and nothing.
Sounds as if that is a better suiting hardware setup for debugging this. Maybe you can also send an image of this setup with the wiring?
The input config in EmulationStation does show 3 controllers connected, and pushing the reset button does trigger it to set up a SNES controller, but the actual controller buttons do nothing.
What about the output of jstest?
I wiped my SD card and reloaded a fresh RetroPie image, did the appropriate updates, and installed & configured the driver again, and still get the same results. Setting it to arcade mode and using a jumper wire on the screws WILL activate the inputs.
That shows that the hardware and the ControlBlock driver are working correctly
There are only two oddities I found while trying to diagnose it. One if that my wireless keyboard (with USB receiver) comes up as js0, so the ControlBlock is on js1 and js2 instead of 0/1.
That should not be a problem. However, I would try to attach as few devices as possible for debugging this issue. Maybe you have a USB keyboard with a cable?
The other is that I can't use the GPIO test script. If I run it while the ControlBlock is connected, the Pi instantly reboots. If I disconnect the ControlBlock and run it, I do get the message, but the system starts shutting down right after the message comes up, so I can't actually test anything.
Sounds like you must stop the ControlBlock driver service via
sudo service controlblockservice stop before running the test script.
I have been getting the lightning bolt a bit as well, but it doesn't seem to work even when the bolt isn't there.
The lighting bolt indicates a low supply voltage. That might lead to an unstable communication with the ControlBlock. I agree with the comments above that this issue should (also) be solved. I would try and start with a USB keyboard with cable to get rid of the bluetooth receiver. We made very good experiences with the official Raspberry Pi power supply.
Hope that gives some ideas for further steps.