Adjust the chain properly including tightening the chain adjusters and rear axle to spec. And then with the chain properly adjusted, go about the task of installing the yamalink without touching the rear axle/chain adjusters. Then measure the chain slack with the yamalink in place and use that as your new measurement for chain slack.
Look at it this way: If you have the chain properly adjusted, you can move the swingarm through the entire arc and the chain will still be properly adjusted.
It might help to think of it as putting some weight on the bike. If the chain was properly adjusted before you put weight on the bike, it will still be properly adjusted after you put weight on the bike. You're not changing the arc itself, you're changing the default position of the swingarm in that arc.