Although nothing prevented the already qualified players from competing in the World Cup, none of them decided to participate (Bacrot and Shirov were not yet fixed, since Kasparov and Kramnik still had time to change their minds). All other players who were't already qualified were there (including unlucky Ivanchuk and Gata Kamsky who came out of retirement in early 2005).
World Cup was played under the same format as 1998-2004 FIDE World Championships were played, only that all rounds consisted of a 2-game mini match, and that this time from round 4 onwards players weren't eliminated, but continued to play-off for places 1-16.
See whole pairing tree here.
According to regulations, first 10 qualified for the Candidates. Since 3rd placed Bacrot qualified by rating, 11th placed Vladimir Malakhov took the final spot in the Candidates.
Among the qualifiers was a 15 year old prodigy Magnus Carlsen who became the youngest person to qualify for the Candidates (breaking Fischer's record - although the cycles are not comparable).