A rod knock isn't a 'top-end issue'. That being said, there are detail differences between '01 & '06. The '06 has variable valve timing that's run by oil pressure. Using an '01 short-block will necessitate the shutting off of the timing feature or supplying oil (externally?) to make the timing work. It could be done if you're 'handy' enough but you may well be better off to find a block that matches the upper end.