I have checked the chain and found it was too tight now done by the book on the side stand which is a complete PITA and measured the slack on the centre stand if i adjust to this measurement will that work?

No, because the weight of the bike needs to be on the rear wheel for proper measurement. Have someone hold the bike upright but still on both wheels if its too difficult to measure on the side stand. 

<my_inner_engineer>Factory suggested method is actually a really bad way to check your chain slack, because static sag affects your chain tension. If you fully preload your rear spring the chain will sit differently and you will get faulty slack measurement</my_inner_engineer>

 

In reality, it doesn't change that much and chain tensioning in general isn't that accurate anyway. Adjust once with yamaha suggested PITA method. Measure again when bike is on a center stand and write down the slack amount some where (it is probably very similar to factory . Now you have measurements for both methods. I always add some slack to factory suggestions. I rather drive with bit too much slack than kill my chain with too little slack. Also check the tightest position on your chain. Sprockets wear unevenly and you can easily over tighten our chain if you're doing your measurements on a loosest spot.