I don't know if the new owner is on here but, just in case he/she is, I hope the following may hewlp:
There is a trick to fitting racks that use the original Yamaha side pieces. If you attempt to fit the rack fully assembled the chances are you will scratch up your rear mudguard or its decals as the fitting plates are narrower than the mudguard they have to pass over.
The easiest way to fit the rack is to (a) loosen off one side, (b) fit the frame fixing bolts/nuts to both side pieces and then (c) tighten the side piece back onto the main rack frame.