In the flow where you create your Email object you also need to create an Attachment object with the create activity and associate it with your Email object. Then you need to copy the PDF to the Attachment object. In the new EmailConnector module there is a Java action CopyAttachmentContent, you might want to implement this, or in the CommunityCommons module the 'DuplicateFileDocument' Java action. Here you can specify source and target files.
Then you can use the IVK_SendEmail flow and the Email with Attachments will get sent.