The above setup is from 2000, so it would have been right around when Make Yourself came out. GREAT album. Probably my favorite Incubus album. Looks like Flanger is not what he used. He has three phasers - two of which are BOSS PH-2's, which I don't care for. They are tone suckers BIG TIME. They totally steal your bass!
he uses a phase 90 on the intro and uses a delay and a ph-2 for i guess the verse. its pretty easy to dial down the sound with the phase 90 from what i remember you just put the rate on like 11:00.
I would also browse guitargeek.com's forums under "complete that rig". Evidently it was illegal for them to post rigs on the site so now they just moved it to the forums. Thats why it only goes to 2004.
I think I found one for Incubus complete with pictures at some point. That site is loaded with good stuff in the forums.
I'm going to go there now, Ill post a link if I find anything.