Flashing qr codes was just a quick hack and actually doesn't work super well. I think if I had more time I would try compressing and stripping down the message more so it would fit in a single qr code instead (like in https://webrtchacks.com/the-minimum-viable-sdp/).
Hey, how serendipitous... I've been trying to do a wiimote project myself and saw your post; do you have any pointers to /resources for troubleshooting the connection to the remote?