Is the difference permanent? did you try too look at his eyes in light and dark environments? If the eyes still look different - I would take him to the vet. Sorry I don't have more information...
Please take your cat to the vet ASAP. The bigger pupil means that the eye is not responding to light - cannot see. Since you mentioned that the third eyelid was up the other day, hopefully this is just an injury. I hate to be an alarmist, but usually it's a bad bad thing. Here's a thread to a similar question: Eye not dilating
Would another recommendation to see a vet be overkill? One evening two years ago or so I noticed that Sabby's third eyelid on one eye was closed even though his eyes were wide open. I rushed him to the emergency vet who checked for scratches and gave me some ointment to use. He was fine, but I don't like to take chances when it comes to eyesight.