To be taken with a grain of salt, the following is my interpretation of what I've found out so far, I'm not a native speaker.

No, they are not completely interchangeable. "Сей" used to be an old demonstrative pronoun for what today is этот, which still exists in some phrases such as до сих пор and as a component of some words. Сейчас means literally "this hour". It can only be used to imply the present or "in a minute". There is a correspondent word тотчас for "that hour", meaning any specific point in time which is not now.

Теперь on the other hand mean "nowadays", "at present". I suppose you can often replace сейчас with теперь, but less frequently the other way round.