If Im not mistaken , you set the number once cyclinder to TPC, check in the timing port to see if it is on the TDC mark there and the look at the cams - It should have two marks to show you if its level to the top of the head ( where the valve cover mates up, Im not sure of how to describe it ) . If its in time the marks will be level, if not, youl lhave to remove the chain and get it level, then put it all back together - Its not uncommon for it to have skipped time, thats where I would start, seeing as how it was just apart. other than that ,make sure your battery is agood an string - at least 12v - before even attempting to start it - alot of Yamahas are very particular to voltage , i.e. FZR600s and RD350s -
Good luck !