this is copied from the poppet valve service manual,
53. GEAR WHEELS.--If the flywheel is removed, see that it is replaced so that the marked teeth mesh with one another. Should a new (unmarked) gear wheel be fitted, mesh the teeth of it so that the exhaust valve closes and the inlet valve opens with the piston at the top (the inlet valves are those in the centre). When so meshed, mark the teeth of the new wheel with a file. A small piece of chalk dropped in the teeth serves to mark them until the file can be applied.
hope this helps
Tom