When the new distributor is seated, the rotor should now be pointing at the mark you made. Insert the new distributor with the rotor pointing the same way as the old rotor did at the point when the drive gear cleared and the shaft stopped rotating.
Note that the shaft will rotate as you remove it (every distributor I've seen has a helical drive gear). Make some sort of mark somewhere on the engine (not the distributor body) to indicate the spot. With the old distributor installed, rotate the crankshaft to the TDC timing mark, remove the distributor cap and note exactly where the rotor is pointing. The first issue is to ensure that the distributor shaft is properly indexed.
