Sorry this is a little late, but I think you can get Trujillo's tone with a Dunlop MXR-80 DI/distortion pedal. In fact, they have setting suggestions in the manual to get Trujillo's tone since he used to (does?) endorse them. He may use SansAmp now. The setting calls for the mid to be cranked up. I can dig up the exact settings if you want, but a lot of the tone comes from the MXR-80 itself with its "color" button. Also, I use the MXR with a Fernandes Gravity Deluxe 4 (with EMG jazz P/Us) and I can get really close to the Trujillo tone he uses with Metallica. Trujillo also endorses Gravity basses. His look a little different than the stock models, though. It looks like his neck his not painted like the body and headstock, still neckthrough, though...BTW, the Gravity is an awesome bass, I've had a lot of people play mine and also give rave reviews of it.
In that vid he is using his Zon signature bass, which he seems to only use for "Sad But True". It might also help to have an Ampeg rig.
But of the gear I've mentioned, I'd look for the MXR-80 to get close to Trujillo's sound without spending thousands. Then again, you could get lucky and find a cheap Gravity Deluxe, like I did.
