In the editor, a few options under "Custom Ability Count", you'll find "Allow Custom Abilities" - you'll need to tell your new class that it has access to the Cleric's custom abilities by selecting Cleric in that list.
There isn't unfortunately a way to pre-select the Knowledge domain (it's a limitation in the way the custom abilities work). What I'd do is to grant 3 domain choices, as you did, then add an eval rule requiring the selection of the Knowledge domain:
(Put this on the Class, in the Eval Rule button on the top left)
Phase: Validation, priority: 5000
Code:
validif (#hasability[cdKnow] <> 0)
Eval Rules are only checked once a thing has been selected, so unlike a pre-req, it won't require you to have selected the Knowledge domain before you select the Cloistered Cleric class. Once you've selected the class, there will be a validation error until the user selects the Knowledge domain.