Most likely there is a timing mark on the fly wheel as well, and it should be able to get the crank set correctly.
and in my experience on engines, there is some type of marking, dots, lines holes to align the gears or chain sprockets on the cam, and if your gong to do a lot of work I would suggest some type of manual that covers the info like that, either the John Deere factory book or at least a after market book,
there are a lot of torque specifications and so on most all bolts of the repair procedure,