You're throwing me off a little here.
You're talking about a "V8" mark on the timing cover, and then you reference the flywheel. Two completely different sides of the fence.
The timing chain and gears get lined up like this:
The Crank-shaft has a key-way in it for the Harmonic balancer. The harmonic balancer gets slid on after placing the timing cover back on.
On the harmonic balancer there is a small groove from front to back that is supposed to line up with the timing tag on the timing cover at TDC.
The second image isn't exact but is the correct concept.
Now, are you pulling my leg? Because I don't see at this point what replacing the heads has to do with the timing.