A Thoth adapter changes a module's type, so it connects to different conduits and rolls different modifiers. Janus adds a port to a portless module. Cipher keys need a Normal module with exactly the right number of ports, and ciphers can't be removed.
What combinations have you pulled off, and which ones were a waste of materials?
Related answers: What does a Thoth adapter do?, How do cipher keys work?, Where do ciphers drop?