to determine how many links you're going to cut off, push the tire as far forward as you can.
after installing the master link, align the rear wheel by using the notches by the axle. measure your slack using the bottom run of the chain. with your finger, push the chain up and down along the part where it gives the most slack. the total movement from pushing up and down should be an inch, + or - an eighth of an inch. Keep in mind that sometimes tightening the axle, once your done adjusting the chain, may affect the chain tightness, so check it again after you have everything tightened up and make adjustments if you have to.
There are vids on youtube on how to adjust a motorcycle chain to help you.