Considering Data Migration:
You will need to do data upgrade to 2009 before you can upgrade to 2013.
So you need to locate the Upgrade Toolkit for NAV 2009, does not matter which service pack (I think).
There you need to go through the data upgrade process from 4.0 to 2009, using Upgrade4002009.1.fob and Upgrade4002009.2.fob.
In this upgrade, you start by converting the database by opening it in 2009, that you have allready done. Then both upgrade steps are done in 2009.
When you go from 2009 to 2013, first step is run in 2009, then the databse is converted (opened in 2013), and then the second step is run.
Object Merging:
I would think you should compare to Cronus 4.0, NOT Cronus 2009, as it seems you don't have NAV 2009 objects. Otherwise, yes, you compare 3 databases: OldCust, OldBase, NewBase, and the outcome is NewCust.