I have written some specifications but I think they do not have an unique identifier (except the name and the ruleset combo); How do you reference a specification? Also , is there a way to link specifications to agile workbench because User stories in agile workbench has unique id like US-3.
No, Specifications cannot be moved to Agile Workbench. Specifications are rules and user stories are case instances, that is the reason their uniqueness differ. Incase you want to link a user story and the specifications written, you can do them by defining an application feature from the application overview page in Designer studio and can associate those rules manually.