The teeth do not line up because when you use the Locking Pin/Tool it is timed at a different spot.
When you use the Fuel Injection Pump Locking Pin/Tool the Fuel Injection Pump is installed with the Pointer showing 15 Degrees ATDC (After Top Dead Center; passed the Compression Stroke on number 1 cylinder) on the Cranshaft Damper degree marks.
This info should be somewhere in our DIY Section.
DIY Repair Links
http://www.peachparts.com/shopforum/forumdisplay.php?f=82
http://www.peachparts.com/Wikka/DoItYourSelf