In order to mark the coupler or flywheel in the correct spot, you'll need to use a TDC dial indicator tool through the spark plug hole. Once installed, you will want to rotate the engine forward & back a few times zeroing the indicator and take some small readings around .005mm or .010mm in each direction. Then you'll need to mark the coupler or flywheel with a fine line pen in relation to a fixed pointer attached to the case at each measurement and locate the equal distance between them to find the true top dead center. Then use this calculation tool:
http://john.rushworth.com/Pics/Piston/ to find the travel distance for each degree of rotation to create your timing marks. If you have a stock stroke Yamaha engine, just enter 68mm for the stroke and 125mm for the stock length rods with the increments set to one or five for your measurements in millimeters for the dial indicator. Then just take the measurements and score your coupler or flywheel with the timing marks for each increment.
Here's an inexpensive dial indicator holding tool made from a spark plug with a thumb screw attachment.