Rear band pin seal

The reason the fitted O-Ring was square in profile is because it is worn & taken on the profile of the sealing area in the case. The fatter O-Ring in the picture is not for the low/rev band lever pivot shaft. Check your overhaul kit again to see if the correct O-Ring is hiding in one of the seals in the kit. I've seen this on numerous occasions. They often get stuck in the speedometer drive seal or the shift shaft seal in the packaging during transport.