I remember a couple of panels where john was in a dream bubble of his house and vriska was messaging him but it was revealed that they were both dead. Was that correct or did I remeber it wrong?

Yeah, that was during the scrapbook panels during the Scratch [o] section, leading up to the Ancestors Story and then to [S] Cascade. Sadly, that Dead John double died soon after during [S] Caliborn: Enter.