I don't think he ever thought they linked him at that point to running SR. He probably just thought they were clueless about that, and were focused solely on the fake IDs. This is shown in his ballzy response to their questioning, "you know, hypothetically, anybody could login to use TOR to anonymously order fake IDs"...
Yeah, I think he just started to believe the whole mythology he'd created around Silk Road and himself - and really, truly believed that he was smarter than federal agents and that anything they ever discovered was nothing he couldn't talk his way out of.
There are just so many things he never seems to have considered - especially that the online world isn't some magical kingdom which exists separately from the real world.