(Now watching it a third time...what is he using to get that effect? It sounds like an LFO or all pitch shifted?)
It's really hard to tell, based on the complexity of his rig, but if I were in his shoes I would get that effect by:
1) ensuring lots overdrive.... overdriving the organ, the moogerfogers (which have drive knobs) and the two leslies ... this makes the sound thick and would ensure that subtle changes in the frequency spectra (in the moogerfooger phaser) are magnified and smoothed in the leslie and the drive stage of the moogerfooger delay which I would place downstream of the phaser.
2) I would use the spread
parameter in the MF 103 phaser almost like opening a filter or a wah pedal. However it is a more subtle effect, essentially acting as a bank of bandpass filters. The lfo amount
on the phaser would be close to zero, so that the spread parameter is doing most of the work as he twists the knob.
He's done a really fine job of creating his unique B3 voice with that rig.