Step 1: Mod SNES Casing - Preparation Stage
Remove the parts of the casing highlighted in green on the pic with the controller front opened up.
In the last picture, it shows the areas you need to trim off the case backing so the BGP100 board will bit in place.
Step 2: Trim the SNES Board Down a Bit
Step 3: Remove the BGP100 Controller Board
The board section with the D-pad can be removed as it is only a contact board that uses the wires to connect to the button presses. The board with the chips on it is the proper controller board.
The D-pad and left shoulder button use a common grounding, however the right shoulder button and the other buttons do not use a common ground, so you need to wire both sets of contacts per button to the SNES board, and keep their contacts unique.
Step 4: Fit in Battery Holder
Notice there is space for a small switch to turn the system on and off, located above the battery holder in the picture.
The bit in the middle of the controller in the first picture should be removed so the clear plastic circle for the LED to shine through (from the BGP100 controller) can be inserted there. It is in the perfect position as when the board is in place (picture 2) the LED on the board is in just the right position.
Step 5: Wire It Up!
Step 6: Make Sure It Is All Ok
Step 7: Test It Works Ok
You notice the on/off switch above the LED window? Looks neat!
Step 8: Video / Demonstration
The same principle was used a while back when making a PSone controller into bluetooth too: