I'm thinking that the Transwarp for the Vengeance came from Scotty (inadvertently). Remember he made the comment "Starfleet took away my transwarp-beaming formula"
. Most likely the Section 31 engineers and scientist used that for the basis for the new propulsion.
Though, shouldn't it have taken the Enterprise several days to get to Kronos?
(For that matter, Vulcan should have been a day or two in the 2009 movie)