You must have after market "halo" lights because the LEDs you speak of aren't standard nor they an option on any Taco. Post some pics of what you're referring to maybe?
Pretty sure my '05 came with a CD manual from the Dealer.As for the diagnostic port, it's a standard OBDII connector. Your scan tool must support CAN protocol to work.
Toyota posts the service manual, TSB's, and other info online at a subscription-based Web site called Toyota Tech Info System (TIS). (http://techinfo.toyota.com) The dealer can sell you paper manuals, but Toyota does not sell CD's or any other electronic media. When you see CD's on sale on eBay, they're bootleg copies of the info on TIS.