Not real familiar with this bike motor, (built over 4500 car motors, no bike motors). As I look at your photo, I do not know which way is the direction of rotation. I do know that the chain looks really loose on the right side of the photo.
If the notch is supposed to be horizontal, that is how it should be. More than likely you made a mistake somewhere. Perhaps you do not have the crank lined up as well as you think. Manufacturers are pretty good at this stuff. While timing marks are seldom "exactly where they are supposed to be" they are most often less than a degree off. They are so close, (usually), that without a dial indicator to TDC the motor, you would never know they were off.
Step back and look at what you have done. Make sure you are looking straight at the timing marks on the crank, make sure you have the cam chain tight on the tension side, etc. It should line up exactly like they say it should.
Now, all that being said, as I sit here and think, have you taken a bunch of meat off the jugs or head? That will change the center to center distance of the cam and crank, but your problem does seem like a little more than that.
Hope this info helps you.
Tom