Mine broke in two. There's been some rubbing against the wheel, or it got stiff and couldn't cope with the folding under the petrol tank. It's just neoprene so the replacement is 3mm insertion rubber from Clark Rubber which has some reinforcing. Replaced ...
Great minds. I suspect it's a bit too long, and the top part bulges backwards during suspension compression connecting with the tyre.
Put the bike on a centre stand or bike lift. Disconnect dog bones. Let the swingarm hang in its lowest position. If there is still okay in the flap you can shorten it until there's no more slack. You might even go a bit shorter, a I'm not sure a completely extended shock has enough travel to get the swingarm that low.
When do you ride with disconnected links? When the wheel's off the ground you have maximum extension (maybe give or take a few mm if there's an internal bump stop).