Computer Trespass Clarification Act of 2004 - Amends the USA PATRIOT Act to: (1) revise the definition of a "computer trespasser" for purposes of provisions concerning the unlawful interception of communications to exclude any person who has any relationship (currently, persons who have a contractual relationship) with the owner or operator of a protected computer permitting access to the computer; (2) require the owner or operator of a protected computer to be attempting to respond to communications activity that threatens the integrity or operation of such computer in order to legally authorize the interception of a computer trespasser's communications; and (3) limit the length of warrantless surveillance to 96 hours. Directs the Attorney General to annually report to the House and Senate Judiciary Committees regarding the use of such provisions.