The cover takes 6 screws, 4 @ 25mm long and 2 @ 40mm long. If your 2 longer ones are both 40s, they should work in that hole .....
One more tip. Yamaha cheaped out on the 2 little Phillips screws they used for the round alternator cover. They used screws 10mm long and they don't grab all the available threads. Switch to slightly longer 12 or 14mm screws there - less chance of stripping the holes that way.
One more tip. Yamaha cheaped out on the 2 little Phillips screws they used for the round alternator cover. They used screws 10mm long and they don't grab all the available threads. Switch to slightly longer 12 or 14mm screws there - less chance of stripping the holes that way.