IIRC , the PDF is the Yamaha Service manual.
As to shifting: is shifter tight on the shaft? Is this with engine running? If yes, support rear tires off of ground, with the engine OFF, rock the wheel back and forth while trying to shift into first or second gear. FYI , one or the other trans shafts has to be moving for it to shift.
If none of above works then remove clutch cover. Check shift star, they are known to come loose. Check the rest of the shift mechanism.
Also make sure clutch is adjusted correctly.