You do not have to worry about which stroke because every cylinder will be on a different stroke. You only have to worry about the marks on the crank and cam sprockets. That will be at the end of the compression stroke for cylinder number one.
To avoid hitting the valves, rotate the crankshaft backward about an eighth revolution from top dead center. That way no piston will be all the way up. Rotate the cams to line up their marks, then rotate the crank in the normal direction to top dead center.
Even if you rotate the cams with the crank at top dead center, you will not damage a valve if it hits a piston if you are turning things by hand. It is when a cam sprocket is off by three or more teeth, and you are cranking the engine with the starter that you will bend valves.
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