Hello,
Thanks for posting your question to this forum.
If I understand correctly, you want to know how to add an inheritance with Entity Framework using database first.
From your description, I am a bit confused about that how the 'Run Custom Tool' will generate classes from the EF-model. As far as I know, if we want to create an inheritance in entity framework using database first, we need to do steps as follow:
- Create a new entity named Kangaroo that has the base type Animal.
- Cut the properties that Kangaroo needs from the Animal to the Kangaroo.
- Right-click the Kangaroo and select Table Mapping.
- Click <Add a Table or View> in the Mapping Details window.
- The <Add a Table or View> field becomes a drop-down list of tables or views to which the selected entity can be mapped.
- Select Animal from the drop-down list.
- The Mapping Details window is updated with default column mappings and an option for adding a condition.
- Click on <Add a Condition>.
- The <Add a Condition> field becomes a drop-down list of columns for which conditions can be set.
- Select Discriminator (a column used to be judge which row belongs to which entity) from the drop-down list.
- In the Operator column of the Mapping Details window, select = from the drop-down list.
In the Value/Property column, type Instructor. The end result should look like this:

For more detail information, there is a link that shows a walkthrough.
http://msdn.microsoft.com/en-us/data/jj618292(v=msdn.10).aspx
If this does not work for you, please let me know.
Regards.
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